BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238317.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 = 3,010,173 number of mapped reads = 2,602,152 (86.45%) number of supplementary alignments = 33,439 (1.11%) number of secondary alignments = 0 number of mapped bases = 166,989,239 bp number of sequenced bases = 166,894,028 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 188,696 duplication rate = 5.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0139 >>>>>>> ACTG content number of A's = 45,941,725 bp (27.53%) number of C's = 31,990,843 bp (19.17%) number of T's = 51,363,103 bp (30.78%) number of G's = 37,554,204 bp (22.5%) number of N's = 44,153 bp (0.03%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,558,600 number of insertions = 13,881 mapped reads with insertion percentage = 0.53% number of deletions = 56,701 mapped reads with deletion percentage = 2.15% homopolymer indels = 44.05% >>>>>>> Coverage mean coverageData = 0.0539X std coverageData = 0.5009X There is a 3.96% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 14619801 0.05865502337103505 0.8964704804914277 chr2 243199373 10608360 0.04362001377363749 0.6350186613815978 chr3 198022430 9984505 0.05042108108662236 0.2901021793516156 chr4 191154276 6388878 0.0334226266536669 0.29150364189068206 chr5 180915260 10212813 0.056450810174885194 0.31062140050576287 chr6 171115067 7133739 0.04168971864996552 0.32452651857048564 chr7 159138663 10761081 0.06762078301487301 0.6240276889382387 chr8 146364022 10621536 0.07256930941676364 0.7173054074178223 chr9 141213431 8455567 0.05987792336835156 0.4719611836793878 chr10 135534747 7670613 0.05659517702866262 0.4781307943077157 chr11 135006516 8324992 0.06166363110947919 0.4397144677482424 chr12 133851895 8668391 0.06476106296440555 0.3423637869577743 chr13 115169878 5355102 0.04649741836142259 0.2809874697842158 chr14 107349540 5944921 0.05537910083266309 0.34573412205351656 chr15 102531392 5419457 0.052856563187984415 0.31617010511950494 chr16 90354753 6485237 0.07177527229807158 0.37980445501510995 chr17 81195210 4260304 0.052469893236312834 0.3332244235278601 chr18 78077248 4592992 0.058826253712221006 0.7915424809188144 chr19 59128983 4781324 0.08086261182608197 0.6933457264295341 chr20 63025520 3929851 0.06235332925456228 0.3349824536678886 chr21 48129895 2809664 0.058376690828018635 0.34873068456238127 chr22 51304566 2259551 0.044041908472629905 0.27023412007833936 chrMT 16571 7079 0.42719208255385915 0.8751676323331413 chrX 155270560 7205376 0.04640529408794558 0.3217179770944153 chrY 59373566 488105 0.008220914337535327 0.24658773608190893