BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716925.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 = 1,321,445 number of mapped reads = 1,231,851 (93.22%) number of supplementary alignments = 30,369 (2.3%) number of secondary alignments = 0 number of mapped bases = 93,781,624 bp number of sequenced bases = 93,746,489 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,781 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.245 >>>>>>> ACTG content number of A's = 22,561,667 bp (24.07%) number of C's = 19,487,323 bp (20.79%) number of T's = 28,665,460 bp (30.58%) number of G's = 23,028,777 bp (24.56%) number of N's = 3,262 bp (0%) GC percentage = 45.35% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 613,196 number of insertions = 8,999 mapped reads with insertion percentage = 0.72% number of deletions = 17,112 mapped reads with deletion percentage = 1.37% homopolymer indels = 37.42% >>>>>>> Coverage mean coverageData = 0.0303X std coverageData = 0.2522X There is a 2.65% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% 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 7764964 0.031153238330347027 0.3358623702587989 chr2 243199373 7841607 0.03224353296338474 0.28968724663519735 chr3 198022430 6090338 0.03075579872441723 0.1942492898504657 chr4 191154276 5851705 0.03061247240945842 0.26796950774662515 chr5 180915260 5465698 0.030211370782099862 0.19303624568351962 chr6 171115067 5281840 0.030867182490715444 0.20120744779998537 chr7 159138663 5079609 0.03191938969601624 0.29648875881577125 chr8 146364022 4766973 0.03256929493232975 0.25831954793453477 chr9 141213431 3912462 0.02770601898342092 0.2258167790812061 chr10 135534747 4639816 0.03423340584389035 0.34562519763813787 chr11 135006516 4226795 0.03130808145586099 0.2542250482570411 chr12 133851895 4194889 0.0313397804341881 0.19953330643020065 chr13 115169878 2757541 0.023943248424731334 0.17147855328615866 chr14 107349540 2811551 0.02619061991322925 0.19909856693845895 chr15 102531392 2721454 0.02654264169162943 0.18113732734891863 chr16 90354753 2939894 0.03253723686234857 0.21656635606381272 chr17 81195210 2660823 0.032770689305440553 0.22548036652811168 chr18 78077248 2475333 0.03170364047667254 0.36198363846697723 chr19 59128983 2036611 0.034443531694093234 0.2741266498736392 chr20 63025520 2143883 0.03401610966478341 0.21653941592267234 chr21 48129895 1275617 0.02650363147478298 0.22835296471595717 chr22 51304566 1289597 0.02513610581950932 0.18128695613178394 chrMT 16571 78038 4.7093114477098545 3.954274022645718 chrX 155270560 5140265 0.033105213248409746 0.2150273445826976 chrY 59373566 334321 0.0056308054665269724 0.23404570085021872