BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926982.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 35,515,794 number of mapped reads = 34,982,910 (98.5%) number of supplementary alignments = 623,763 (1.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,562,289 number of mapped paired reads (second in pair) = 17,420,621 number of mapped paired reads (both in pair) = 34,668,832 number of mapped paired reads (singletons) = 314,078 number of mapped bases = 3,297,683,518 bp number of sequenced bases = 3,295,229,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,973,976 duplication rate = 6.5% >>>>>>> Insert size mean insert size = 179,089.7881 std insert size = 4,158,022.1813 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 53.2967 >>>>>>> ACTG content number of A's = 924,030,899 bp (28.04%) number of C's = 677,884,512 bp (20.57%) number of T's = 937,500,557 bp (28.45%) number of G's = 755,518,977 bp (22.93%) number of N's = 294,369 bp (0.01%) GC percentage = 43.5% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 30,537,065 number of insertions = 529,654 mapped reads with insertion percentage = 1.49% number of deletions = 1,711,108 mapped reads with deletion percentage = 4.77% homopolymer indels = 52.42% >>>>>>> Coverage mean coverageData = 1.0652X std coverageData = 4.2131X There is a 35.84% of reference with a coverageData >= 1X There is a 21.94% of reference with a coverageData >= 2X There is a 13.85% of reference with a coverageData >= 3X There is a 9.26% of reference with a coverageData >= 4X There is a 6.37% of reference with a coverageData >= 5X There is a 4.49% of reference with a coverageData >= 6X There is a 3.22% of reference with a coverageData >= 7X There is a 2.35% of reference with a coverageData >= 8X There is a 1.73% of reference with a coverageData >= 9X There is a 1.3% of reference with a coverageData >= 10X There is a 0.98% of reference with a coverageData >= 11X There is a 0.74% of reference with a coverageData >= 12X There is a 0.57% of reference with a coverageData >= 13X There is a 0.44% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.21% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 276824635 1.1106276641934625 4.823395937069189 chr2 243199373 286486346 1.177989657070374 7.478022436214423 chr3 198022430 222647723 1.124356079258294 2.2599927454063486 chr4 191154276 194193300 1.0158982789377937 3.734257375145803 chr5 180915260 196998001 1.088896541950082 2.2023348236668054 chr6 171115067 185198001 1.0823009583370002 2.927884540144468 chr7 159138663 169973097 1.0680817206564064 3.1230924467237724 chr8 146364022 152618365 1.0427314234368334 2.6621794644128394 chr9 141213431 139470992 0.9876609541481929 5.473960030760436 chr10 135534747 164009614 1.2100927447040573 6.125646823172136 chr11 135006516 159727998 1.183113250622659 3.9415685968544882 chr12 133851895 146821118 1.0968923376094153 2.5888387073797263 chr13 115169878 97682003 0.8481558259530326 2.003269801777732 chr14 107349540 98775359 0.9201283862045426 2.1587423591341515 chr15 102531392 99894698 0.9742840319577443 2.2485811423800413 chr16 90354753 111705531 1.2362994451437437 7.983281051413862 chr17 81195210 89886554 1.1070425706146951 3.083991621930609 chr18 78077248 89166091 1.1420239991040668 5.810479583257446 chr19 59128983 54925733 0.9289138796789385 3.4562046877746537 chr20 63025520 83424383 1.3236603680540835 2.755884381730055 chr21 48129895 43266886 0.8989607394738759 3.427314159011455 chr22 51304566 44390826 0.8652412340843113 2.2344467136304558 chrMT 16571 149896 9.045682215919378 6.979708280008563 chrX 155270560 183262744 1.1802800479369688 2.675879982321102 chrY 59373566 6183624 0.10414776164867712 3.608406397587437