scripture output

[nimmi]

We did RNA-seq on 5 cases and 5 controls. Following the documentation given on scripture website I got some results for Chr1. Below are few lines from the output. There are a total of 64K rows for Chr1, of which ~62K have FWER<0.05 and last column (Poisson pvalue) is significant for all the rows. Why are so many transcripts significant? Did anyone else observe this trend in their data?

chrom chromStart chromEnd name score strand thickStart thickEnd itemRgb blockCount blockSizes blockStarts Family wise error rate (FWER) at the observed score Read enrichment (average reads per base over transcript / genome average) Total reads aligned transcript Average reads per base over transcript RPKM Genome average reads per base Transcript length Poisson nominal p-value for the observed count given the genome-wide average
chr1 569913 570307 chr1:569913-570307 40848.5882 + 569913 570307 0,0,0 6 1,2,1,7,4,53, 0,3,7,9,17,341, 1.11E-16 10181.53598 109494 1610.205882 40848.5882 0.158149604 68 0
chr1 16266622 16302620 chr1:16266622-16302620 68.37972491 - 16266622 16302620 0,0,0 15 2125,111,210,131,117,88,301,143,613,192,141,189,203,87,143, 0,2203,2401,2936,3471,3680,4172,4569,4809,5521,6026,6807,8167,32911,35855, 1.11E-16 17.0436889 12922 2.695452649 68.37972491 0.158149604 4794 0
chr1 16266622 16302620 chr1:16266622-16302620 68.36914145 - 16266622 16302620 0,0,0 15 2125,111,210,131,122,83,301,143,613,192,141,189,203,87,143, 0,2203,2401,2936,3471,3685,4172,4569,4809,5521,6026,6807,8167,32911,35855, 1.11E-16 17.04105096 12920 2.695035461 68.36914145 0.158149604 4794 0

thanks in advance,
Nirmala