BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548998.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 8,534,327 number of mapped reads = 7,359,742 (86.24%) number of secondary alignments = 0 number of mapped bases = 292,079,744 bp number of sequenced bases = 292,046,340 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 577,397 duplication rate = 7.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1642 >>>>>>> ACTG content number of A's = 88,306,141 bp (30.24%) number of C's = 57,553,139 bp (19.71%) number of T's = 87,894,393 bp (30.1%) number of G's = 58,289,954 bp (19.96%) number of N's = 2,713 bp (0%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 891,401 number of insertions = 8,986 mapped reads with insertion percentage = 0.12% number of deletions = 25,574 mapped reads with deletion percentage = 0.35% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.0944X std coverageData = 0.8611X There is a 7.29% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 23364239 0.09373793696586216 1.1847366904836396 chr2 243199373 25632050 0.10539521415624702 0.554335649425403 chr3 198022430 20795226 0.1050144976000951 0.3985797571629189 chr4 191154276 20738296 0.10848983571782617 0.4441207753960489 chr5 180915260 18953593 0.10476503198237672 0.40457731180201406 chr6 171115067 17542299 0.10251755913463774 0.46006977709534613 chr7 159138663 16354246 0.10276727032701036 0.8232792430355523 chr8 146364022 15588877 0.10650757465519771 2.8736386265467355 chr9 141213431 12476274 0.08835047708740962 0.5139984493197439 chr10 135534747 13942049 0.10286697181793537 0.5963307547503429 chr11 135006516 13505845 0.10003846777291846 0.5124519730366016 chr12 133851895 13613507 0.10170574723652587 0.4110230338239158 chr13 115169878 10011863 0.0869312633985772 0.3586162572669485 chr14 107349540 9190736 0.08561504781482995 0.4414447347356066 chr15 102531392 8331775 0.08126072256972772 0.34755379541283504 chr16 90354753 7593971 0.0840461707642541 0.3996489404308211 chr17 81195210 6893576 0.08490126449577506 0.39779758680218424 chr18 78077248 7936075 0.10164388734602942 1.0701656640473796 chr19 59128983 4687293 0.07927234263440655 0.9102472262300102 chr20 63025520 5808476 0.0921606993484544 0.39901296091718724 chr21 48129895 3865852 0.08032122239202891 0.4273359854629728 chr22 51304566 2884677 0.05622651597910408 0.3101449797449193 chrMT 16571 15982 0.964455977309758 1.3866100041151144 chrX 155270560 9729627 0.06266240683359421 0.39358796746746433 chrY 59373566 2623340 0.04418363552561421 0.47256459317702637