BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472520.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,441,230 number of mapped reads = 14,213,509 (98.42%) number of supplementary alignments = 54,220 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,136,544 number of mapped paired reads (second in pair) = 7,076,965 number of mapped paired reads (both in pair) = 14,105,814 number of mapped paired reads (singletons) = 107,695 number of mapped bases = 1,400,210,468 bp number of sequenced bases = 1,400,032,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,596,914 duplication rate = 45.2% >>>>>>> Insert size mean insert size = 28,785.5543 std insert size = 1,694,195.9338 median insert size = 244 >>>>>>> Mapping quality mean mapping quality = 55.2241 >>>>>>> ACTG content number of A's = 391,350,453 bp (27.95%) number of C's = 310,718,189 bp (22.19%) number of T's = 389,324,626 bp (27.81%) number of G's = 308,423,171 bp (22.03%) number of N's = 216,376 bp (0.02%) GC percentage = 44.22% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 8,993,630 number of insertions = 81,524 mapped reads with insertion percentage = 0.57% number of deletions = 74,261 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.3% >>>>>>> Coverage mean coverageData = 0.4523X std coverageData = 15.4741X There is a 4.58% of reference with a coverageData >= 1X There is a 1.97% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 115737459 0.46434170769829297 14.032260331916671 chr2 243199373 88237984 0.36282159329415703 12.574158137377898 chr3 198022430 167597481 0.846356046635727 23.019008025496113 chr4 191154276 63771860 0.3336146139885461 14.812955903078295 chr5 180915260 66971535 0.37018179118776384 10.715327506644567 chr6 171115067 95161970 0.5561285260753807 15.162974491313486 chr7 159138663 66936712 0.4206187907963007 13.962361305946592 chr8 146364022 52065838 0.35572839068333334 11.669816557569769 chr9 141213431 99186207 0.7023850797874884 19.60378150716687 chr10 135534747 33117127 0.24434418282420226 9.492361091337768 chr11 135006516 78355223 0.5803810462007626 26.824214996622057 chr12 133851895 68644598 0.5128399414890614 15.33226047061569 chr13 115169878 32993172 0.2864739684798485 11.093867924330434 chr14 107349540 51349371 0.47833806274344537 22.203895308543583 chr15 102531392 42292278 0.4124812623240305 14.200289070021933 chr16 90354753 52342169 0.5792962435523453 15.439179848405361 chr17 81195210 44995950 0.5541700058414776 11.918162390007565 chr18 78077248 19798595 0.25357700875932515 7.838381089564826 chr19 59128983 40433801 0.6838237180571836 21.29523912596335 chr20 63025520 23423492 0.3716509122019144 9.734900909480647 chr21 48129895 6875425 0.14285144399338498 5.292346367399145 chr22 51304566 9831538 0.1916308579630125 6.668935944931572 chrMT 16571 3460 0.20879850340957093 0.6883408443419818 chrX 155270560 74530589 0.48000463835513957 14.971013033232863 chrY 59373566 5556634 0.09358767502696402 7.945288856299193