BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504621.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 543,755,692 number of mapped reads = 495,326,978 (91.09%) number of supplementary alignments = 4,752,758 (0.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 246,265,319 number of mapped paired reads (second in pair) = 249,061,659 number of mapped paired reads (both in pair) = 480,108,240 number of mapped paired reads (singletons) = 15,218,738 number of mapped bases = 47,511,309,117 bp number of sequenced bases = 47,470,909,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 184,751,467 duplication rate = 27.12% >>>>>>> Insert size mean insert size = 97,435.3591 std insert size = 2,926,064.3999 median insert size = 329 >>>>>>> Mapping quality mean mapping quality = 52.2147 >>>>>>> ACTG content number of A's = 12,642,165,120 bp (26.63%) number of C's = 10,943,565,838 bp (23.05%) number of T's = 12,795,441,442 bp (26.95%) number of G's = 10,937,258,269 bp (23.04%) number of N's = 152,478,739 bp (0.32%) GC percentage = 46.09% >>>>>>> Mismatches and indels general error rate = 0.0183 number of mismatches = 813,003,709 number of insertions = 13,639,503 mapped reads with insertion percentage = 2.56% number of deletions = 12,250,219 mapped reads with deletion percentage = 2.31% homopolymer indels = 34.31% >>>>>>> Coverage mean coverageData = 15.3475X std coverageData = 354.5768X There is a 87.25% of reference with a coverageData >= 1X There is a 82.19% of reference with a coverageData >= 2X There is a 76.83% of reference with a coverageData >= 3X There is a 71.65% of reference with a coverageData >= 4X There is a 66.73% of reference with a coverageData >= 5X There is a 62.15% of reference with a coverageData >= 6X There is a 57.89% of reference with a coverageData >= 7X There is a 53.96% of reference with a coverageData >= 8X There is a 50.33% of reference with a coverageData >= 9X There is a 46.97% of reference with a coverageData >= 10X There is a 43.85% of reference with a coverageData >= 11X There is a 40.96% of reference with a coverageData >= 12X There is a 38.27% of reference with a coverageData >= 13X There is a 35.76% of reference with a coverageData >= 14X There is a 33.42% of reference with a coverageData >= 15X There is a 31.23% of reference with a coverageData >= 16X There is a 29.19% of reference with a coverageData >= 17X There is a 27.27% of reference with a coverageData >= 18X There is a 25.48% of reference with a coverageData >= 19X There is a 23.81% of reference with a coverageData >= 20X There is a 22.24% of reference with a coverageData >= 21X There is a 20.77% of reference with a coverageData >= 22X There is a 19.4% of reference with a coverageData >= 23X There is a 18.12% of reference with a coverageData >= 24X There is a 16.93% of reference with a coverageData >= 25X There is a 15.81% of reference with a coverageData >= 26X There is a 14.76% of reference with a coverageData >= 27X There is a 13.79% of reference with a coverageData >= 28X There is a 12.88% of reference with a coverageData >= 29X There is a 12.03% of reference with a coverageData >= 30X There is a 11.24% of reference with a coverageData >= 31X There is a 10.51% of reference with a coverageData >= 32X There is a 9.82% of reference with a coverageData >= 33X There is a 9.18% of reference with a coverageData >= 34X There is a 8.59% of reference with a coverageData >= 35X There is a 8.03% of reference with a coverageData >= 36X There is a 7.52% of reference with a coverageData >= 37X There is a 7.04% of reference with a coverageData >= 38X There is a 6.59% of reference with a coverageData >= 39X There is a 6.17% of reference with a coverageData >= 40X There is a 5.79% of reference with a coverageData >= 41X There is a 5.42% of reference with a coverageData >= 42X There is a 5.09% of reference with a coverageData >= 43X There is a 4.78% of reference with a coverageData >= 44X There is a 4.49% of reference with a coverageData >= 45X There is a 4.22% of reference with a coverageData >= 46X There is a 3.97% of reference with a coverageData >= 47X There is a 3.73% of reference with a coverageData >= 48X There is a 3.51% of reference with a coverageData >= 49X There is a 3.31% of reference with a coverageData >= 50X There is a 3.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3673124673 14.736672102413738 108.9757468524855 chr2 243199373 3732629532 15.348022842147707 342.61247071672193 chr3 198022430 2543212281 12.843051572491056 32.70618232094851 chr4 191154276 3560293504 18.62523600570672 994.4687786002004 chr5 180915260 2472372656 13.66591550099201 45.08938549860828 chr6 171115067 2038152473 11.911005317842642 44.011516426249024 chr7 159138663 2343158290 14.724003870762694 51.52435054010239 chr8 146364022 2231823622 15.248444197577461 261.2769095898736 chr9 141213431 1738888358 12.313902053693463 125.77212220841078 chr10 135534747 3116279643 22.992477663310943 787.1651809243642 chr11 135006516 2044986600 15.147317778350788 42.74229732196016 chr12 133851895 1903154413 14.218359874546415 26.55114968592864 chr13 115169878 1061608456 9.217761401119136 19.940679899722745 chr14 107349540 1271842974 11.84767977580528 41.49744273831783 chr15 102531392 1389013283 13.547200090680521 22.889061593658635 chr16 90354753 2131877435 23.594524518261924 276.4391145200061 chr17 81195210 1634027628 20.124680113519013 102.0208660718301 chr18 78077248 1075219899 13.771232036764411 410.76562809037165 chr19 59128983 1595682503 26.9864696133874 60.007427877109826 chr20 63025520 1218329248 19.330729012628534 242.42342416777802 chr21 48129895 788066134 16.373734744278998 327.5566100723655 chr22 51304566 882210802 17.195561151418765 41.60236053478308 chrMT 16571 17920809 1081.4560980025346 512.4709500542631 chrX 155270560 2326414457 14.982972026377698 30.105022838431715 chrY 59373566 721019444 12.143778664060703 822.7389685571294