BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068167.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 = 1,434,934 number of mapped reads = 1,206,279 (84.07%) number of supplementary alignments = 10,220 (0.71%) number of secondary alignments = 0 number of mapped bases = 79,310,580 bp number of sequenced bases = 79,268,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,728 duplication rate = 9.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.635 >>>>>>> ACTG content number of A's = 22,481,886 bp (28.36%) number of C's = 14,846,309 bp (18.73%) number of T's = 24,896,215 bp (31.41%) number of G's = 16,956,807 bp (21.39%) number of N's = 87,310 bp (0.11%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 718,056 number of insertions = 5,580 mapped reads with insertion percentage = 0.46% number of deletions = 23,689 mapped reads with deletion percentage = 1.94% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.0256X std coverageData = 0.3647X There is a 1.22% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 6843330 0.027455618656211895 0.6381151946373661 chr2 243199373 6906081 0.028396787848626568 0.4043500512794248 chr3 198022430 3892490 0.01965681362459798 0.2645680299072569 chr4 191154276 6386542 0.03341040615800821 0.3323830186568559 chr5 180915260 4700385 0.02598114166820422 0.29505908142087195 chr6 171115067 3137113 0.018333353427024635 0.262460418560319 chr7 159138663 5234585 0.03289323223734763 0.4057177354430378 chr8 146364022 3717979 0.025402274064318893 0.391358099261543 chr9 141213431 3551967 0.025153181073831427 0.3420472237659011 chr10 135534747 3452054 0.025469881904158494 0.3916625225593134 chr11 135006516 2882333 0.02134958434154393 0.29836495816939046 chr12 133851895 3186110 0.02380324910603619 0.2875401978556873 chr13 115169878 1594367 0.013843611087267107 0.224266630271119 chr14 107349540 2681855 0.024982454512613654 0.2912323060662742 chr15 102531392 3920610 0.038238142714379614 0.34539096707474803 chr16 90354753 1917742 0.021224583503648115 0.2691583432565865 chr17 81195210 1452434 0.017888173452596526 0.2498105705899634 chr18 78077248 1480898 0.018967087569479908 0.44026967002737527 chr19 59128983 1879025 0.031778408906508675 0.3939309398365116 chr20 63025520 2452733 0.038916505567903284 0.3612232262251201 chr21 48129895 1670548 0.034709155297346896 0.3351183892284166 chr22 51304566 1156812 0.022547934622427174 0.2568984903669285 chrMT 16571 16030 0.9673526039466538 1.629770198814983 chrX 155270560 4965660 0.03198069228319908 0.3357220219048763 chrY 59373566 230897 0.0038888855016725793 0.1361459621550196