BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237832.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 = 2,689,851 number of mapped reads = 2,264,380 (84.18%) number of supplementary alignments = 27,430 (1.02%) number of secondary alignments = 0 number of mapped bases = 155,821,358 bp number of sequenced bases = 155,733,291 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 442,770 duplication rate = 13.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8478 >>>>>>> ACTG content number of A's = 44,497,907 bp (28.57%) number of C's = 29,556,220 bp (18.98%) number of T's = 48,197,946 bp (30.95%) number of G's = 33,214,490 bp (21.33%) number of N's = 266,728 bp (0.17%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,427,619 number of insertions = 13,236 mapped reads with insertion percentage = 0.58% number of deletions = 48,195 mapped reads with deletion percentage = 2.09% homopolymer indels = 44.91% >>>>>>> Coverage mean coverageData = 0.0503X std coverageData = 0.8906X There is a 1.18% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 13660301 0.054805484316125336 1.2445157435109169 chr2 243199373 11650010 0.04790312514498136 0.8991491170036053 chr3 198022430 9834742 0.0496647879737664 0.7682080178056928 chr4 191154276 10061497 0.05263547962693756 0.8561706177842224 chr5 180915260 10253018 0.05667304129015983 0.8219148226420671 chr6 171115067 8889034 0.05194769902991652 0.8364400533544603 chr7 159138663 8288006 0.052080404873076004 0.9269785738087358 chr8 146364022 7727920 0.052799314301433996 1.120429305242042 chr9 141213431 6678796 0.04729575616642301 0.8499987420712908 chr10 135534747 8486597 0.06261565530498242 1.067421748271785 chr11 135006516 5700866 0.04222659889986347 0.7473714338081441 chr12 133851895 7765780 0.05801770680945533 0.7957011401135996 chr13 115169878 5080256 0.044110978393152415 0.7078815702064226 chr14 107349540 6071626 0.05655940398067844 0.7917360750165646 chr15 102531392 4450698 0.04340814957432744 0.7075105696266271 chr16 90354753 3829020 0.04237762677520683 0.7050179668925064 chr17 81195210 3455555 0.04255860659760594 0.7218689887341025 chr18 78077248 3019924 0.0386786685924176 1.1999629154951557 chr19 59128983 3105249 0.05251652983782928 0.948208529080984 chr20 63025520 4949341 0.07852915771262181 0.924346060904031 chr21 48129895 2664057 0.05535139854346244 0.7878825346683259 chr22 51304566 1798480 0.03505496957132431 0.6161844376794967 chrMT 16571 40359 2.4355198841349344 4.577099876581266 chrX 155270560 7724209 0.04974677105563347 0.7697753077231726 chrY 59373566 636017 0.01071212397786584 0.4426908181464232