BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472732.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 = 17,284,288 number of mapped reads = 17,126,139 (99.09%) number of supplementary alignments = 61,070 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,596,564 number of mapped paired reads (second in pair) = 8,529,575 number of mapped paired reads (both in pair) = 17,024,402 number of mapped paired reads (singletons) = 101,737 number of mapped bases = 1,690,795,080 bp number of sequenced bases = 1,690,558,234 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,704,114 duplication rate = 47.49% >>>>>>> Insert size mean insert size = 25,997.5604 std insert size = 1,588,991.8185 median insert size = 254 >>>>>>> Mapping quality mean mapping quality = 55.2292 >>>>>>> ACTG content number of A's = 469,471,254 bp (27.77%) number of C's = 377,693,860 bp (22.34%) number of T's = 467,803,084 bp (27.67%) number of G's = 375,264,510 bp (22.2%) number of N's = 325,526 bp (0.02%) GC percentage = 44.54% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 10,792,980 number of insertions = 101,669 mapped reads with insertion percentage = 0.59% number of deletions = 99,747 mapped reads with deletion percentage = 0.58% homopolymer indels = 45.18% >>>>>>> Coverage mean coverageData = 0.5462X std coverageData = 17.9435X There is a 4.83% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 173708169 0.6969217099764016 19.670906330620568 chr2 243199373 138298153 0.5686616346663032 19.253454148697205 chr3 198022430 168479727 0.8508113298074365 20.34950394312622 chr4 191154276 72920279 0.38147343876314854 13.584667102914029 chr5 180915260 81963415 0.4530486538283172 13.743293516343417 chr6 171115067 112866708 0.6595953820945528 18.20974052496168 chr7 159138663 74686632 0.46931795575032575 14.400239381549339 chr8 146364022 71496786 0.48848607070937144 16.787412554737266 chr9 141213431 126244356 0.8939968040292144 33.86404744615044 chr10 135534747 51639253 0.38100379528505707 15.990187562632261 chr11 135006516 80224339 0.5942256816700611 18.82516373534069 chr12 133851895 99791343 0.7455355264114863 22.50548270972467 chr13 115169878 31427725 0.2728814647177103 9.090145594757217 chr14 107349540 39610559 0.36898676044629536 15.274121175179207 chr15 102531392 45726428 0.44597490688510305 17.448475695979532 chr16 90354753 46965806 0.5197934191685523 11.602856656051163 chr17 81195210 56984431 0.7018201073684026 16.468554499253713 chr18 78077248 25342596 0.32458362261948576 12.056898844944156 chr19 59128983 30812990 0.5211148312833319 13.095068258350981 chr20 63025520 38274379 0.6072838272496601 17.786440766256813 chr21 48129895 7557653 0.1570261684551774 8.02099041131774 chr22 51304566 17171258 0.334692588569992 8.923138756275282 chrMT 16571 1631 0.09842495926618793 0.37307783001974093 chrX 155270560 94982467 0.6117223187705384 20.678361508798798 chrY 59373566 3617997 0.06093615802022065 2.5190939144574127