BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008732.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 = 3,656,106 number of mapped reads = 3,339,149 (91.33%) number of supplementary alignments = 25,423 (0.7%) number of secondary alignments = 0 number of mapped bases = 219,573,005 bp number of sequenced bases = 219,454,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 184,984 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6219 >>>>>>> ACTG content number of A's = 58,962,507 bp (26.87%) number of C's = 40,752,357 bp (18.57%) number of T's = 68,909,598 bp (31.4%) number of G's = 50,660,847 bp (23.08%) number of N's = 169,172 bp (0.08%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,824,094 number of insertions = 16,301 mapped reads with insertion percentage = 0.48% number of deletions = 71,430 mapped reads with deletion percentage = 2.11% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 0.0709X std coverageData = 0.5304X There is a 5.58% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 20064409 0.08049893283916833 0.9832962826784387 chr2 243199373 22160874 0.09112224972718165 0.7228496093768495 chr3 198022430 16628026 0.08397041688661229 0.35484611232908814 chr4 191154276 11173976 0.05845527619795437 0.3165630342821412 chr5 180915260 10240119 0.05660174271645189 0.28977581278640074 chr6 171115067 12507182 0.07309223097227317 0.38276678792715224 chr7 159138663 10323681 0.06487223661040811 0.7287403615271955 chr8 146364022 13258350 0.09058476132884624 0.5442869733966601 chr9 141213431 6580882 0.046602380194274866 0.411504261077773 chr10 135534747 12426774 0.09168699743099827 0.5064043842245336 chr11 135006516 8936030 0.06618962006248647 0.5230655909985726 chr12 133851895 8522612 0.06367195623192336 0.31007772848250525 chr13 115169878 5986194 0.0519770803265069 0.2751781808092618 chr14 107349540 7861354 0.07323137108924734 0.34128048794250054 chr15 102531392 6496846 0.06336445719960576 0.32415610346023943 chr16 90354753 5983426 0.06622148588021706 0.35629836242573176 chr17 81195210 6600007 0.08128566943788926 0.42601593522474834 chr18 78077248 3834400 0.04911033749550189 0.7853906187725278 chr19 59128983 4708474 0.0796305595176565 0.6923877975887673 chr20 63025520 5080120 0.08060417430907353 0.3558688138009817 chr21 48129895 2602558 0.054073627212359386 0.3015179257612094 chr22 51304566 2812114 0.054812158434397434 0.28015527580036426 chrMT 16571 54538 3.291171323396295 3.164184432551841 chrX 155270560 14148862 0.09112391943456635 0.4149386994163681 chrY 59373566 581197 0.009788817468029459 0.22851331652983106