[BioC] calcNormFactors gives NaN normalization values- Please Help!

Thu Dec 19 22:15:06 CET 2013

Hi Audra,

Your dataset looks pretty sparse (a lot of 0s), which is ok but it could be due to this:

----
?calcNormFactors

If ‘refColumn’ is unspecified, the library whose upper quartile is closest to the mean upper quartile is used.
----

As you can see, many of your upper quartiles are 0 or 1 and this might mess up the "closest to the mean" calculation.

I suggest three things:

1. Remove rows with all zeros, mostly zeros or features without some number of samples greater than some cutoff on CPM.

2. Specify 'refColumn', perhaps to a library with lots of reads.

3. Have a look at some MA plots to make sure there is some semblance of a funnel-shaped plot that would suggest TMM is going to work.  I'd be nervous about blowing through a standard analysis when you have library sizes ranging from 70k to 4M; definitely worth some extra care and spot checks.

Cheers, Mark

----------
Prof. Dr. Mark Robinson
Bioinformatics, Institute of Molecular Life Sciences
University of Zurich
http://ow.ly/riRea

On 19.12.2013, at 19:07, Audra [guest] <guest at bioconductor.org> wrote:

> 
> I have already posted this once but I really haven't found a solution yet.  Every time I try to normalize my data, the norm.factors I get back are NaN.  I have succeeded at normalization before with a different data set.  The data, to explain, are replicates of SI at different time points.  I need to normalize using the TMM (default method).  I have copied and pasted my session below.  Thanks so much!
> 
>> library(edgeR)
> Loading required package: limma
>> targets <- read.delim("/users/Audra/desktop/targets.txt")
>> targets
>                                                                                                           files
> 1                 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_0h_31_lane2_pRNA-A_10_1 trimmed RNA-Seq.txt
> 2                 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak5_0H_42_lane2_pRNA-A_17_1 trimmed RNA-Seq.txt
> 3                 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_0h_47_lane2_pRNA-A_20_1 trimmed RNA-Seq.txt
> 4                     /users/Audra/desktop/SI_Tabdelim_for_R/Si_0h_AI6_HiSeq_3_2011_s1_bar_K trimmed RNA-Seq.txt
> 5                     /users/Audra/desktop/SI_Tabdelim_for_R/Si_0h_AJ6_HiSeq_3_2011_s1_bar_B trimmed RNA-Seq.txt
> 6                      /users/Audra/desktop/SI_Tabdelim_for_R/SI_Ai8_0h_37_lane2_pRNA-A_14_1 trimmed RNA-Seq.txt
> 7                      /users/Audra/desktop/SI_Tabdelim_for_R/SI_Ai11_0h_11_lane3_pRNA-B_3_1 trimmed RNA-Seq.txt
> 8                      /users/Audra/desktop/SI_Tabdelim_for_R/SI_U25_0h_33_lane2_pRNA-A_11_1 trimmed RNA-Seq.txt
> 9    /users/Audra/desktop/SI_Tabdelim_for_R/SI-A_0h_AF2_June2011_50SR_s_3_SS02.txt.s14_bar_C trimmed RNA-Seq.txt
> 10  /users/Audra/desktop/SI_Tabdelim_for_R/Si-A_10d_W22_June2011_50SR_s_3_SS02.txt.s21_bar_L trimmed RNA-Seq.txt
> 11  /users/Audra/desktop/SI_Tabdelim_for_R/Si-A_12h_Ak4_June2011_50SR_s_2_SS01.txt.s10_bar_O trimmed RNA-Seq.txt
> 12 /users/Audra/desktop/SI_Tabdelim_for_R/SI-A_12h_Ak10_June2011_50SR_s_2_SS01.txt.s12_bar_S trimmed RNA-Seq.txt
> 13               /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ai24_1h_2_lane2_pRNA-A_1_1-1 trimmed RNA-Seq.txt
> 14                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_1h_35_lane3_pRNA-B_17_1 trimmed RNA-Seq.txt
> 15                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_1h_48_lane3_pRNA-B_20_1 trimmed RNA-Seq.txt
> 16                   /users/Audra/desktop/SI_Tabdelim_for_R/Si_24h_Z12_HiSeq_3_2011_s1_bar_N trimmed RNA-Seq.txt
> 17         /users/Audra/desktop/SI_Tabdelim_for_R/Si_24h_Z14_Jan_2011_PE120_SP03_s_7_1_bar_C trimmed RNA-Seq.txt
> 18                    /users/Audra/desktop/SI_Tabdelim_for_R/SI_V43_24h_26_lane3_pRNA-B_12_1 trimmed RNA-Seq.txt
> 19                     /users/Audra/desktop/SI_Tabdelim_for_R/SI_Z18_24h_10_lane3_pRNA-B_2_1 trimmed RNA-Seq.txt
> 20  /users/Audra/desktop/SI_Tabdelim_for_R/SI-A_24h_W20_June2011_50SR_s_3_SS02.txt.s16_bar_F trimmed RNA-Seq.txt
> 21   /users/Audra/desktop/SI_Tabdelim_for_R/Si-B_24h_S6_June2011_50SR_s_3_SS02.txt.s17_bar_G trimmed RNA-Seq.txt
> 22               /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ai24_2h_3_lane2_pRNA-A_2_1-1 trimmed RNA-Seq.txt
> 23                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_2h_39_lane3_pRNA-B_18_1 trimmed RNA-Seq.txt
> 24                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_2h_23_lane3_pRNA-B_11_1 trimmed RNA-Seq.txt
> 25                 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ai24_4h_4_lane2_pRNA-A_3_1 trimmed RNA-Seq.txt
> 26                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_4h_40_lane2_pRNA-A_16_1 trimmed RNA-Seq.txt
> 27                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak5_4h_45_lane2_pRNA-A_18_1 trimmed RNA-Seq.txt
> 28                 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_4h_24_lane2_pRNA-A_8_1 trimmed RNA-Seq.txt
> 29                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_6h_41_lane3_pRNA-B_19_1 trimmed RNA-Seq.txt
> 30                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak5_6h_46_lane2_pRNA-A_19_1 trimmed RNA-Seq.txt
> 31                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_6h_7_lane2_pRNA-A_4_1-1 trimmed RNA-Seq.txt
> 32    /users/Audra/desktop/SI_Tabdelim_for_R/SI-A_6h_AJ7_June2011_50SR_s_2_SS01.txt.s4_bar_F trimmed RNA-Seq.txt
> 33   /users/Audra/desktop/SI_Tabdelim_for_R/SI-A_6h_Ak25_June2011_50SR_s_2_SS01.txt.s6_bar_H trimmed RNA-Seq.txt
> 34                    /users/Audra/desktop/SI_Tabdelim_for_R/Si_96h_Y5_HiSeq_3_2011_s1_bar_E trimmed RNA-Seq.txt
> 35      /users/Audra/desktop/SI_Tabdelim_for_R/Si_96h_Y18_May2011_120PE_s_3_1_TC05.txt.bar_F trimmed RNA-Seq.txt
> 36         /users/Audra/desktop/SI_Tabdelim_for_R/Si_96h_Y23_Jan_2011_PE120_SP03_s_7_1_bar_G trimmed RNA-Seq.txt
> 37                      /users/Audra/desktop/SI_Tabdelim_for_R/SI_Y24_96h_5_lane3_pRNA-B_1_1 trimmed RNA-Seq.txt
> 38  /users/Audra/desktop/SI_Tabdelim_for_R/Si-A_96h_V40_June2011_50SR_s_3_SS02.txt.s19_bar_J trimmed RNA-Seq.txt
>   group description
> 1     0h     Prox SI
> 2     0h     Prox SI
> 3     0h     Prox SI
> 4     0h          Si
> 5     0h          Si
> 6     0h          Si
> 7     0h          Si
> 8     0h          Si
> 9     0h          Si
> 10   10d          Si
> 11   12h          Si
> 12   12h          Si
> 13    1h     Prox SI
> 14    1h     Prox SI
> 15    1h     Prox SI
> 16   24h          Si
> 17   24h          Si
> 18   24h          Si
> 19   24h          Si
> 20   24h          Si
> 21   24h          Si
> 22    2h     Prox SI
> 23    2h     Prox SI
> 24    2h     Prox SI
> 25    4h     Prox SI
> 26    4h     Prox SI
> 27    4h     Prox SI
> 28    4h     Prox SI
> 29    6h     Prox SI
> 30    6h     Prox SI
> 31    6h     Prox SI
> 32    6h          Si
> 33    6h          Si
> 34   96h          Si
> 35   96h          Si
> 36   96h          Si
> 37   96h          Si
> 38   96h          Si
>> d <- readDGE(targets)
>> d
> An object of class "DGEList"
> $samples
>                                                                                           files
> 1 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_0h_31_lane2_pRNA-A_10_1 trimmed RNA-Seq.txt
> 2 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak5_0H_42_lane2_pRNA-A_17_1 trimmed RNA-Seq.txt
> 3 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_0h_47_lane2_pRNA-A_20_1 trimmed RNA-Seq.txt
> 4     /users/Audra/desktop/SI_Tabdelim_for_R/Si_0h_AI6_HiSeq_3_2011_s1_bar_K trimmed RNA-Seq.txt
> 5     /users/Audra/desktop/SI_Tabdelim_for_R/Si_0h_AJ6_HiSeq_3_2011_s1_bar_B trimmed RNA-Seq.txt
>  group description lib.size norm.factors
> 1    0h     Prox SI   374815            1
> 2    0h     Prox SI   747066            1
> 3    0h     Prox SI   168922            1
> 4    0h          Si  1503428            1
> 5    0h          Si  3945244            1
> 33 more rows ...
> 
> $counts
>                                                                                                                                                                                                                     1
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  23
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      5
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                     2
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  30
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     26
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  4
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      1
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                     3
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  11
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  4
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                       4
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1165
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       28
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|    3
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                       5
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1122
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       67
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|    2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                      6
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  448
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       9
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                       7
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1452
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                        2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|    2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                      8
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  322
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       8
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                     9
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  33
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     10
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     1
>                                                                                                                                                                                                                    10
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  38
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                     11
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  218
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   9
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                    12
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  11
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      0
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    13
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                   9
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      5
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    14
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  90
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      7
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  3
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    15
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                   0
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      0
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                     16
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  937
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      31
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   6
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      1
>                                                                                                                                                                                                                      17
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1200
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       43
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|    0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                    18
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  99
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      6
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                     19
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  715
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      13
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                    20
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  30
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     11
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  4
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    21
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  21
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      7
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0| 12
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    22
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                   8
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    23
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  66
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     15
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      1
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    24
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  12
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      4
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      1
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    25
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  63
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     13
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      2
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    26
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  17
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      8
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    27
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  21
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      1
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    28
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  25
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      7
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  3
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    29
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  54
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     11
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    30
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  12
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      0
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    31
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  13
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      3
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      1
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     2
>                                                                                                                                                                                                                     32
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  277
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       7
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   3
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                     33
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  148
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       5
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   4
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                      34
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  2172
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       17
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   17
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                      35
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1535
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       26
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   13
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                      36
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1508
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       41
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|    1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                     37
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  562
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      34
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   3
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                    38
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  62
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      9
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     3
> 50765 more rows ...
> 
>> d$samples
>                                                                                                           files
> 1                 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_0h_31_lane2_pRNA-A_10_1 trimmed RNA-Seq.txt
> 2                 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak5_0H_42_lane2_pRNA-A_17_1 trimmed RNA-Seq.txt
> 3                 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_0h_47_lane2_pRNA-A_20_1 trimmed RNA-Seq.txt
> 4                     /users/Audra/desktop/SI_Tabdelim_for_R/Si_0h_AI6_HiSeq_3_2011_s1_bar_K trimmed RNA-Seq.txt
> 5                     /users/Audra/desktop/SI_Tabdelim_for_R/Si_0h_AJ6_HiSeq_3_2011_s1_bar_B trimmed RNA-Seq.txt
> 6                      /users/Audra/desktop/SI_Tabdelim_for_R/SI_Ai8_0h_37_lane2_pRNA-A_14_1 trimmed RNA-Seq.txt
> 7                      /users/Audra/desktop/SI_Tabdelim_for_R/SI_Ai11_0h_11_lane3_pRNA-B_3_1 trimmed RNA-Seq.txt
> 8                      /users/Audra/desktop/SI_Tabdelim_for_R/SI_U25_0h_33_lane2_pRNA-A_11_1 trimmed RNA-Seq.txt
> 9    /users/Audra/desktop/SI_Tabdelim_for_R/SI-A_0h_AF2_June2011_50SR_s_3_SS02.txt.s14_bar_C trimmed RNA-Seq.txt
> 10  /users/Audra/desktop/SI_Tabdelim_for_R/Si-A_10d_W22_June2011_50SR_s_3_SS02.txt.s21_bar_L trimmed RNA-Seq.txt
> 11  /users/Audra/desktop/SI_Tabdelim_for_R/Si-A_12h_Ak4_June2011_50SR_s_2_SS01.txt.s10_bar_O trimmed RNA-Seq.txt
> 12 /users/Audra/desktop/SI_Tabdelim_for_R/SI-A_12h_Ak10_June2011_50SR_s_2_SS01.txt.s12_bar_S trimmed RNA-Seq.txt
> 13               /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ai24_1h_2_lane2_pRNA-A_1_1-1 trimmed RNA-Seq.txt
> 14                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_1h_35_lane3_pRNA-B_17_1 trimmed RNA-Seq.txt
> 15                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_1h_48_lane3_pRNA-B_20_1 trimmed RNA-Seq.txt
> 16                   /users/Audra/desktop/SI_Tabdelim_for_R/Si_24h_Z12_HiSeq_3_2011_s1_bar_N trimmed RNA-Seq.txt
> 17         /users/Audra/desktop/SI_Tabdelim_for_R/Si_24h_Z14_Jan_2011_PE120_SP03_s_7_1_bar_C trimmed RNA-Seq.txt
> 18                    /users/Audra/desktop/SI_Tabdelim_for_R/SI_V43_24h_26_lane3_pRNA-B_12_1 trimmed RNA-Seq.txt
> 19                     /users/Audra/desktop/SI_Tabdelim_for_R/SI_Z18_24h_10_lane3_pRNA-B_2_1 trimmed RNA-Seq.txt
> 20  /users/Audra/desktop/SI_Tabdelim_for_R/SI-A_24h_W20_June2011_50SR_s_3_SS02.txt.s16_bar_F trimmed RNA-Seq.txt
> 21   /users/Audra/desktop/SI_Tabdelim_for_R/Si-B_24h_S6_June2011_50SR_s_3_SS02.txt.s17_bar_G trimmed RNA-Seq.txt
> 22               /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ai24_2h_3_lane2_pRNA-A_2_1-1 trimmed RNA-Seq.txt
> 23                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_2h_39_lane3_pRNA-B_18_1 trimmed RNA-Seq.txt
> 24                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_2h_23_lane3_pRNA-B_11_1 trimmed RNA-Seq.txt
> 25                 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ai24_4h_4_lane2_pRNA-A_3_1 trimmed RNA-Seq.txt
> 26                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_4h_40_lane2_pRNA-A_16_1 trimmed RNA-Seq.txt
> 27                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak5_4h_45_lane2_pRNA-A_18_1 trimmed RNA-Seq.txt
> 28                 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_4h_24_lane2_pRNA-A_8_1 trimmed RNA-Seq.txt
> 29                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_6h_41_lane3_pRNA-B_19_1 trimmed RNA-Seq.txt
> 30                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak5_6h_46_lane2_pRNA-A_19_1 trimmed RNA-Seq.txt
> 31                /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_6h_7_lane2_pRNA-A_4_1-1 trimmed RNA-Seq.txt
> 32    /users/Audra/desktop/SI_Tabdelim_for_R/SI-A_6h_AJ7_June2011_50SR_s_2_SS01.txt.s4_bar_F trimmed RNA-Seq.txt
> 33   /users/Audra/desktop/SI_Tabdelim_for_R/SI-A_6h_Ak25_June2011_50SR_s_2_SS01.txt.s6_bar_H trimmed RNA-Seq.txt
> 34                    /users/Audra/desktop/SI_Tabdelim_for_R/Si_96h_Y5_HiSeq_3_2011_s1_bar_E trimmed RNA-Seq.txt
> 35      /users/Audra/desktop/SI_Tabdelim_for_R/Si_96h_Y18_May2011_120PE_s_3_1_TC05.txt.bar_F trimmed RNA-Seq.txt
> 36         /users/Audra/desktop/SI_Tabdelim_for_R/Si_96h_Y23_Jan_2011_PE120_SP03_s_7_1_bar_G trimmed RNA-Seq.txt
> 37                      /users/Audra/desktop/SI_Tabdelim_for_R/SI_Y24_96h_5_lane3_pRNA-B_1_1 trimmed RNA-Seq.txt
> 38  /users/Audra/desktop/SI_Tabdelim_for_R/Si-A_96h_V40_June2011_50SR_s_3_SS02.txt.s19_bar_J trimmed RNA-Seq.txt
>   group description lib.size norm.factors
> 1     0h     Prox SI   374815            1
> 2     0h     Prox SI   747066            1
> 3     0h     Prox SI   168922            1
> 4     0h          Si  1503428            1
> 5     0h          Si  3945244            1
> 6     0h          Si   796503            1
> 7     0h          Si  1110495            1
> 8     0h          Si   369702            1
> 9     0h          Si   945932            1
> 10   10d          Si   478680            1
> 11   12h          Si   930415            1
> 12   12h          Si    34830            1
> 13    1h     Prox SI   177704            1
> 14    1h     Prox SI   830511            1
> 15    1h     Prox SI   896926            1
> 16   24h          Si  1926498            1
> 17   24h          Si  3401008            1
> 18   24h          Si   673436            1
> 19   24h          Si   592641            1
> 20   24h          Si  1270874            1
> 21   24h          Si  1271765            1
> 22    2h     Prox SI   238914            1
> 23    2h     Prox SI   930402            1
> 24    2h     Prox SI   854939            1
> 25    4h     Prox SI   751449            1
> 26    4h     Prox SI   264237            1
> 27    4h     Prox SI  1540281            1
> 28    4h     Prox SI  1637729            1
> 29    6h     Prox SI   552252            1
> 30    6h     Prox SI    71195            1
> 31    6h     Prox SI  1522576            1
> 32    6h          Si   873977            1
> 33    6h          Si  1611862            1
> 34   96h          Si  1900171            1
> 35   96h          Si  2088219            1
> 36   96h          Si  1009910            1
> 37   96h          Si   865353            1
> 38   96h          Si   500564            1
>> summary(d$counts)
>       1                   2                  3           
> Min.   :    0.000   Min.   :    0.00   Min.   :   0.000  
> 1st Qu.:    0.000   1st Qu.:    0.00   1st Qu.:   0.000  
> Median :    0.000   Median :    0.00   Median :   0.000  
> Mean   :    7.383   Mean   :   14.71   Mean   :   3.327  
> 3rd Qu.:    1.000   3rd Qu.:    1.00   3rd Qu.:   0.000  
> Max.   :20468.000   Max.   :20880.00   Max.   :7082.000  
>       4                  5                   6           
> Min.   :    0.00   Min.   :     0.00   Min.   :    0.00  
> 1st Qu.:    0.00   1st Qu.:     0.00   1st Qu.:    0.00  
> Median :    0.00   Median :     0.00   Median :    0.00  
> Mean   :   29.61   Mean   :    77.71   Mean   :   15.69  
> 3rd Qu.:    2.00   3rd Qu.:     0.00   3rd Qu.:    1.00  
> Max.   :85570.00   Max.   :113242.00   Max.   :26749.00  
>       7                  8                  9           
> Min.   :    0.00   Min.   :   0.000   Min.   :    0.00  
> 1st Qu.:    0.00   1st Qu.:   0.000   1st Qu.:    0.00  
> Median :    0.00   Median :   0.000   Median :    0.00  
> Mean   :   21.87   Mean   :   7.282   Mean   :   18.63  
> 3rd Qu.:    0.00   3rd Qu.:   1.000   3rd Qu.:    1.00  
> Max.   :30148.00   Max.   :8501.000   Max.   :32736.00  
>       10                  11                 12                13        
> Min.   :    0.000   Min.   :    0.00   Min.   :  0.000   Min.   :   0.0  
> 1st Qu.:    0.000   1st Qu.:    0.00   1st Qu.:  0.000   1st Qu.:   0.0  
> Median :    0.000   Median :    0.00   Median :  0.000   Median :   0.0  
> Mean   :    9.428   Mean   :   18.33   Mean   :  0.686   Mean   :   3.5  
> 3rd Qu.:    0.000   3rd Qu.:    1.00   3rd Qu.:  0.000   3rd Qu.:   0.0  
> Max.   :19060.000   Max.   :42038.00   Max.   :997.000   Max.   :8224.0  
>       14                 15                 16          
> Min.   :    0.00   Min.   :    0.00   Min.   :    0.00  
> 1st Qu.:    0.00   1st Qu.:    0.00   1st Qu.:    0.00  
> Median :    0.00   Median :    0.00   Median :    0.00  
> Mean   :   16.36   Mean   :   17.67   Mean   :   37.95  
> 3rd Qu.:    2.00   3rd Qu.:    1.00   3rd Qu.:    2.00  
> Max.   :41561.00   Max.   :25430.00   Max.   :48180.00  
>       17                  18                 19          
> Min.   :     0.00   Min.   :    0.00   Min.   :    0.00  
> 1st Qu.:     0.00   1st Qu.:    0.00   1st Qu.:    0.00  
> Median :     0.00   Median :    0.00   Median :    0.00  
> Mean   :    66.99   Mean   :   13.26   Mean   :   11.67  
> 3rd Qu.:     1.00   3rd Qu.:    1.00   3rd Qu.:    1.00  
> Max.   :101736.00   Max.   :17818.00   Max.   :14039.00  
>       20                 21                 22           
> Min.   :    0.00   Min.   :    0.00   Min.   :    0.000  
> 1st Qu.:    0.00   1st Qu.:    0.00   1st Qu.:    0.000  
> Median :    0.00   Median :    0.00   Median :    0.000  
> Mean   :   25.03   Mean   :   25.05   Mean   :    4.706  
> 3rd Qu.:    1.00   3rd Qu.:    1.00   3rd Qu.:    0.000  
> Max.   :54657.00   Max.   :34765.00   Max.   :10297.000  
>       23                 24                 25                26           
> Min.   :    0.00   Min.   :    0.00   Min.   :    0.0   Min.   :    0.000  
> 1st Qu.:    0.00   1st Qu.:    0.00   1st Qu.:    0.0   1st Qu.:    0.000  
> Median :    0.00   Median :    0.00   Median :    0.0   Median :    0.000  
> Mean   :   18.33   Mean   :   16.84   Mean   :   14.8   Mean   :    5.205  
> 3rd Qu.:    2.00   3rd Qu.:    1.00   3rd Qu.:    1.0   3rd Qu.:    1.000  
> Max.   :44889.00   Max.   :28549.00   Max.   :26033.0   Max.   :14323.000  
>       27                 28                 29                 30          
> Min.   :    0.00   Min.   :    0.00   Min.   :    0.00   Min.   :   0.000  
> 1st Qu.:    0.00   1st Qu.:    0.00   1st Qu.:    0.00   1st Qu.:   0.000  
> Median :    0.00   Median :    0.00   Median :    0.00   Median :   0.000  
> Mean   :   30.34   Mean   :   32.26   Mean   :   10.88   Mean   :   1.402  
> 3rd Qu.:    2.00   3rd Qu.:    2.00   3rd Qu.:    1.00   3rd Qu.:   0.000  
> Max.   :40600.00   Max.   :53032.00   Max.   :24632.00   Max.   :5736.000  
>       31                 32                 33                 34          
> Min.   :    0.00   Min.   :    0.00   Min.   :    0.00   Min.   :    0.00  
> 1st Qu.:    0.00   1st Qu.:    0.00   1st Qu.:    0.00   1st Qu.:    0.00  
> Median :    0.00   Median :    0.00   Median :    0.00   Median :    0.00  
> Mean   :   29.99   Mean   :   17.21   Mean   :   31.75   Mean   :   37.43  
> 3rd Qu.:    2.00   3rd Qu.:    1.00   3rd Qu.:    2.00   3rd Qu.:    1.00  
> Max.   :47530.00   Max.   :18676.00   Max.   :54499.00   Max.   :59323.00  
>       35                 36                 37          
> Min.   :    0.00   Min.   :    0.00   Min.   :    0.00  
> 1st Qu.:    0.00   1st Qu.:    0.00   1st Qu.:    0.00  
> Median :    0.00   Median :    0.00   Median :    0.00  
> Mean   :   41.13   Mean   :   19.89   Mean   :   17.04  
> 3rd Qu.:    3.00   3rd Qu.:    0.00   3rd Qu.:    1.00  
> Max.   :60187.00   Max.   :30252.00   Max.   :38192.00  
>       38           
> Min.   :    0.000  
> 1st Qu.:    0.000  
> Median :    0.000  
> Mean   :    9.859  
> 3rd Qu.:    1.000  
> Max.   :10764.000  
>> d <- calcNormFactors(d)
>> d
> An object of class "DGEList"
> $samples
>                                                                                           files
> 1 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak2_0h_31_lane2_pRNA-A_10_1 trimmed RNA-Seq.txt
> 2 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak5_0H_42_lane2_pRNA-A_17_1 trimmed RNA-Seq.txt
> 3 /users/Audra/desktop/SI_Tabdelim_for_R/Prox_SI_Ak8_0h_47_lane2_pRNA-A_20_1 trimmed RNA-Seq.txt
> 4     /users/Audra/desktop/SI_Tabdelim_for_R/Si_0h_AI6_HiSeq_3_2011_s1_bar_K trimmed RNA-Seq.txt
> 5     /users/Audra/desktop/SI_Tabdelim_for_R/Si_0h_AJ6_HiSeq_3_2011_s1_bar_B trimmed RNA-Seq.txt
>  group description lib.size norm.factors
> 1    0h     Prox SI   374815          NaN
> 2    0h     Prox SI   747066          NaN
> 3    0h     Prox SI   168922          NaN
> 4    0h          Si  1503428          NaN
> 5    0h          Si  3945244          NaN
> 33 more rows ...
> 
> $counts
>                                                                                                                                                                                                                     1
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  23
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      5
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                     2
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  30
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     26
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  4
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      1
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                     3
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  11
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  4
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                       4
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1165
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       28
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|    3
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                       5
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1122
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       67
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|    2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                      6
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  448
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       9
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                       7
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1452
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                        2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|    2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                      8
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  322
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       8
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                     9
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  33
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     10
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     1
>                                                                                                                                                                                                                    10
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  38
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                     11
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  218
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   9
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                    12
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  11
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      0
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    13
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                   9
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      5
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    14
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  90
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      7
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  3
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    15
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                   0
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      0
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                     16
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  937
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      31
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   6
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      1
>                                                                                                                                                                                                                      17
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1200
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       43
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|    0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                    18
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  99
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      6
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                     19
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  715
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      13
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                    20
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  30
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     11
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  4
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    21
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  21
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      7
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0| 12
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    22
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                   8
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    23
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  66
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     15
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      1
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    24
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  12
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      4
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      1
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    25
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  63
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     13
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      2
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    26
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  17
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      8
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    27
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  21
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      2
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  2
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      1
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    28
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  25
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      7
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  3
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    29
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  54
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                     11
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    30
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  12
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      0
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     0
>                                                                                                                                                                                                                    31
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  13
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      3
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      1
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     2
>                                                                                                                                                                                                                     32
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  277
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       7
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   3
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                     33
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  148
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       5
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   4
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                      34
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  2172
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       17
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   17
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                      35
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1535
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       26
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   13
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                      36
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  1508
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                       41
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|    1
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                        0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                       0
>                                                                                                                                                                                                                     37
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  562
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      34
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|   3
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                       0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                      0
>                                                                                                                                                                                                                    38
> maker-Contig6333-snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470|                                                  62
> maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603|                      9
> maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|  0
> maker-Contig3008-pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0|                      0
> maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0|                     3
> 50765 more rows ...
> 
>> 
> 
> -- output of sessionInfo(): 
> 
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] edgeR_3.4.2  limma_3.18.6
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor