BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238526.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,788,625 number of mapped reads = 2,428,902 (87.1%) number of supplementary alignments = 21,843 (0.78%) number of secondary alignments = 0 number of mapped bases = 149,650,217 bp number of sequenced bases = 149,578,450 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 557,102 duplication rate = 17.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3468 >>>>>>> ACTG content number of A's = 36,732,975 bp (24.56%) number of C's = 26,681,315 bp (17.84%) number of T's = 49,768,257 bp (33.27%) number of G's = 36,385,921 bp (24.33%) number of N's = 9,982 bp (0.01%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 870,350 number of insertions = 8,924 mapped reads with insertion percentage = 0.36% number of deletions = 42,264 mapped reads with deletion percentage = 1.72% homopolymer indels = 41.23% >>>>>>> Coverage mean coverageData = 0.0483X std coverageData = 0.6361X There is a 2.7% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 14784975 0.05931770577213527 0.6977273535803709 chr2 243199373 5222648 0.021474759311982273 1.5150783833131096 chr3 198022430 6003916 0.030319373416435702 0.2899076904939032 chr4 191154276 2741705 0.014342891288500394 0.18711642475136817 chr5 180915260 5553848 0.030698615473343707 0.28729416067053115 chr6 171115067 8800259 0.05142889608896919 0.5775195898536477 chr7 159138663 18578161 0.11674196986309983 0.7928141058786287 chr8 146364022 13413261 0.09164315667685055 0.5902542127908346 chr9 141213431 3968090 0.028099947518448156 0.3439822267941775 chr10 135534747 4917760 0.036284127198761805 0.3791955127106603 chr11 135006516 10104493 0.07484448380254476 0.5427865452846753 chr12 133851895 7638061 0.05706352532401577 0.39799940327346855 chr13 115169878 7363062 0.06393218546259118 0.4772068414201726 chr14 107349540 1701975 0.015854516004446782 0.22430306974830191 chr15 102531392 1514289 0.014769028006564077 0.3155871791664377 chr16 90354753 6794831 0.07520169968258339 0.4964872790694517 chr17 81195210 2446204 0.030127442246901018 0.30929557344507186 chr18 78077248 2500439 0.03202519381830671 0.960152223489802 chr19 59128983 4035197 0.0682439777460742 0.5520019842856483 chr20 63025520 3834326 0.06083767337421413 0.4184377976528771 chr21 48129895 1088686 0.02261974600193913 0.25921325265643136 chr22 51304566 978834 0.01907888666283621 0.22102329334563572 chrMT 16571 51171 3.0879850340957096 3.1335657653818365 chrX 155270560 15170609 0.09770434910520062 0.5382815768417408 chrY 59373566 443417 0.007468256159651923 0.21676896078640276