BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008715.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 = 1,493,486 number of mapped reads = 1,082,182 (72.46%) number of supplementary alignments = 5,160 (0.35%) number of secondary alignments = 0 number of mapped bases = 73,484,244 bp number of sequenced bases = 73,453,398 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,973 duplication rate = 1.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7572 >>>>>>> ACTG content number of A's = 22,488,206 bp (30.62%) number of C's = 12,978,130 bp (17.67%) number of T's = 21,400,617 bp (29.13%) number of G's = 16,574,854 bp (22.57%) number of N's = 11,591 bp (0.02%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 673,402 number of insertions = 5,068 mapped reads with insertion percentage = 0.46% number of deletions = 19,391 mapped reads with deletion percentage = 1.77% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.1848X There is a 2.24% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 6304585 0.02529415964825219 0.24413129299815478 chr2 243199373 6648203 0.027336431496474294 0.24012647767007478 chr3 198022430 5946856 0.03003122424060749 0.18000708149040484 chr4 191154276 4345121 0.02273096417680973 0.15728578550819486 chr5 180915260 3162752 0.01748195260035002 0.13662007103407814 chr6 171115067 4203842 0.024567339824026133 0.17069471137306236 chr7 159138663 3876537 0.02435949207390287 0.1918983194858988 chr8 146364022 5125167 0.03501657668303212 0.2379585961428146 chr9 141213431 2576799 0.018247548988452805 0.15576760304593373 chr10 135534747 3753521 0.027694160228889497 0.19632315722991744 chr11 135006516 3152303 0.0233492656013729 0.17433359622479797 chr12 133851895 3115757 0.023277645789026746 0.15820770123664568 chr13 115169878 2160782 0.018761693921391494 0.14164884480260073 chr14 107349540 2589617 0.024123224002636622 0.16479308625760072 chr15 102531392 1890837 0.018441542274194426 0.14150244994459535 chr16 90354753 1770975 0.01960024172718396 0.15311603115437888 chr17 81195210 2005089 0.024694671028007688 0.168741181415783 chr18 78077248 1519583 0.0194625584139441 0.2327026759332996 chr19 59128983 1201712 0.020323569576699806 0.1725457055705898 chr20 63025520 1601319 0.025407469863001526 0.16677849091558464 chr21 48129895 881785 0.018320941693307245 0.14456580691127896 chr22 51304566 941218 0.018345696560419202 0.1407948696136367 chrMT 16571 14682 0.8860056725604972 1.2158958841664342 chrX 155270560 4537718 0.029224587069177826 0.18346930935718186 chrY 59373566 157484 0.0026524261655430973 0.0651609113601121