The same qvalue in Cuffdiff

[whfwind]

Hi All,

I just finished tophat-cuffdiff pipeline, and I found there are many same q value in my DEGs list as below: 1 gene Cola hira1a foldchange pvalue qvalue
2 AT1G04770 5.60882 48.5309 3.11313 5e-05 0.01297
3 AT1G07135 3.7599 140.164 5.22028 5e-05 0.01297
4 AT1G07450 3.26493 28.8261 3.14225 5e-05 0.01297
5 AT1G09070 61.0794 332.8 2.4459 5e-05 0.01297
6 AT1G12610 0 7.0099 inf 5e-05 0.01297
7 AT1G14200 24.793 120.2 2.27743 5e-05 0.01297
8 AT1G15405 822.018 128.763 -2.67445 5e-05 0.01297
9 AT1G18300 4.11828 111.759 4.76221 5e-05 0.01297
10 AT1G18740 10.5067 49.4091 2.23347 5e-05 0.01297
11 AT1G19180 5.07474 48.2497 3.24911 5e-05 0.01297
12 AT1G19770 8.73901 41.3665 2.24292 5e-05 0.01297
13 AT1G23710 4.16688 35.4204 3.08754 5e-05 0.01297
14 AT1G27730 2.08797 168.621 6.33554 5e-05 0.01297
15 AT1G32640 20.2656 121.766 2.58701 5e-05 0.01297
16 AT1G32920 8.83319 272.146 4.9453 5e-05 0.01297
17 AT1G32928 4.66117 86.0303 4.20608 5e-05 0.01297
18 AT1G36370 5.9179 29.1226 2.29898 5e-05 0.01297
19 AT1G50735 0 15.5932 inf 5e-05 0.01297
20 AT1G60190 1.76243 39.109 4.47187 5e-05 0.01297

is there any problem? my commands are below:
#tophat -p 6 -o Cola /home/whf/Athaliana/genome/bowtie2_index_At Cola_1.clean.fq.gz Cola_2.clean.fq.gz

tophat -p 6 -o hira1a /home/whf/Athaliana/genome/bowtie2_index_At hira1a_1.clean.fq.gz hira1a_2.clean.fq.gz

cuffdiff -o cuffdiff_TE_repa -p 6 -L Cola,hira1a /home/whf/Athaliana/annotation/TAIR10_GFF3_genes_transposons.gff Cola/accepted_hits.bam hira1a/accepted_hits.bam

Thank you all