BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525008.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,931,177 number of mapped reads = 1,773,181 (91.82%) number of supplementary alignments = 5,551 (0.29%) number of secondary alignments = 0 number of mapped bases = 103,093,776 bp number of sequenced bases = 103,060,091 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,771 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1139 >>>>>>> ACTG content number of A's = 25,903,247 bp (25.13%) number of C's = 20,120,112 bp (19.52%) number of T's = 32,196,782 bp (31.24%) number of G's = 24,839,110 bp (24.1%) number of N's = 840 bp (0%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 517,857 number of insertions = 6,320 mapped reads with insertion percentage = 0.35% number of deletions = 20,339 mapped reads with deletion percentage = 1.14% homopolymer indels = 43.35% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.3179X There is a 3.01% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 11208614 0.044969252052535505 0.6714784333909186 chr2 243199373 9594368 0.03945062802443985 0.3491263387464319 chr3 198022430 5797529 0.029277132898530737 0.1885510057224455 chr4 191154276 6732213 0.03521874132703157 0.2212414514263953 chr5 180915260 4576743 0.02529771673213194 0.17543560760858015 chr6 171115067 6212406 0.03630542949207389 0.31347772846315614 chr7 159138663 6689745 0.04203720751380197 0.4222387516747383 chr8 146364022 6220336 0.04249907808627997 0.2946563257608253 chr9 141213431 2618107 0.018540070738738725 0.22008346897099104 chr10 135534747 5391607 0.03978025649761976 0.31235930205761003 chr11 135006516 4461657 0.03304771600801846 0.26683451865069474 chr12 133851895 5755737 0.04300078829664683 0.22658682746414113 chr13 115169878 2007717 0.01743265717447404 0.14350782859977687 chr14 107349540 2424709 0.02258704601808261 0.16813410912928656 chr15 102531392 2932754 0.028603473948739525 0.196557347381542 chr16 90354753 3412519 0.037768007622133615 0.22303224568086888 chr17 81195210 2723227 0.03353925681083896 0.27226859923232377 chr18 78077248 2054862 0.02631832003095191 0.36757344813524623 chr19 59128983 2599278 0.04395945724282117 0.3883447704496871 chr20 63025520 1980389 0.03142201762079869 0.19543822160711694 chr21 48129895 1510518 0.03138419479203102 0.201930995107569 chr22 51304566 1452782 0.02831681686967199 0.18044934966820286 chrMT 16571 19061 1.1502625067889687 1.308932073562534 chrX 155270560 4428514 0.028521272802777293 0.22333032377081677 chrY 59373566 288384 0.004857110991110084 0.1247727458020908