BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237586.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 = 2,565,527 number of mapped reads = 2,080,377 (81.09%) number of supplementary alignments = 11,600 (0.45%) number of secondary alignments = 0 number of mapped bases = 131,249,420 bp number of sequenced bases = 131,172,890 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 132,391 duplication rate = 4.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.3085 >>>>>>> ACTG content number of A's = 33,557,573 bp (25.58%) number of C's = 24,989,027 bp (19.05%) number of T's = 39,512,746 bp (30.12%) number of G's = 33,083,000 bp (25.22%) number of N's = 30,544 bp (0.02%) GC percentage = 44.27% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,238,824 number of insertions = 12,396 mapped reads with insertion percentage = 0.59% number of deletions = 46,347 mapped reads with deletion percentage = 2.2% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.393X There is a 3.28% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 11090743 0.044496350522633205 0.502595011474985 chr2 243199373 11379566 0.04679109925172381 0.569311142442703 chr3 198022430 9028336 0.04559249171924615 0.3003552955273789 chr4 191154276 8116654 0.042461273531751914 0.31557388976681366 chr5 180915260 7270991 0.040190037037229474 0.26815799316740413 chr6 171115067 7025234 0.0410556131798727 0.3172919783398023 chr7 159138663 7604453 0.04778507533395577 0.5593793847608592 chr8 146364022 7013003 0.04791480108410795 0.3732643867532526 chr9 141213431 5492108 0.038892249562295526 0.4193888071231263 chr10 135534747 5790659 0.04272453469072399 0.3952083248807435 chr11 135006516 5428334 0.04020794077820659 0.40836531263634884 chr12 133851895 7521525 0.0561928914043391 0.34792302858324275 chr13 115169878 4195068 0.03642504509729532 0.2681145755098975 chr14 107349540 3819804 0.03558286323350803 0.298560397766938 chr15 102531392 4055259 0.03955138929548523 0.2905634146358957 chr16 90354753 3604627 0.039894160299458734 0.3201598442190826 chr17 81195210 3396014 0.041825299792931134 0.30582614837947586 chr18 78077248 3318931 0.042508298960537136 0.6002995929450216 chr19 59128983 2776691 0.046959897822020716 0.4090486519840676 chr20 63025520 2720774 0.04316940185499461 0.3013212362702066 chr21 48129895 1669081 0.0346786752807169 0.2904029644673894 chr22 51304566 1542610 0.030067694169754793 0.244506485871381 chrMT 16571 127342 7.684629774907972 6.374899019654136 chrX 155270560 6777225 0.043647842836401184 0.32053555111023374 chrY 59373566 484388 0.008158310720295965 0.1997784980702534