BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238253.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 = 2,283,770 number of mapped reads = 2,048,106 (89.68%) number of supplementary alignments = 19,840 (0.87%) number of secondary alignments = 0 number of mapped bases = 133,635,671 bp number of sequenced bases = 133,572,907 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,622 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4983 >>>>>>> ACTG content number of A's = 37,550,596 bp (28.11%) number of C's = 26,552,745 bp (19.88%) number of T's = 39,124,467 bp (29.29%) number of G's = 30,313,536 bp (22.69%) number of N's = 31,563 bp (0.02%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,179,485 number of insertions = 11,532 mapped reads with insertion percentage = 0.56% number of deletions = 37,754 mapped reads with deletion percentage = 1.82% homopolymer indels = 44.03% >>>>>>> Coverage mean coverageData = 0.0432X std coverageData = 0.4133X There is a 3.83% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% 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 0.01% 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 13564268 0.05442019741246703 0.708639762269948 chr2 243199373 10294225 0.04232833692379626 0.5334773538214194 chr3 198022430 7463498 0.03769016469497925 0.21325039067001228 chr4 191154276 8771460 0.04588681029557508 0.25860047014553106 chr5 180915260 10036143 0.05547427563600771 0.2606757717118631 chr6 171115067 7669653 0.044821611179335835 0.2910622432928483 chr7 159138663 7234083 0.04545773392604159 0.6124956013331735 chr8 146364022 6250073 0.04270224960065664 0.47024081354079866 chr9 141213431 4984093 0.035294751814365304 0.4125690492498515 chr10 135534747 6034924 0.04452676626164359 0.4237867087326009 chr11 135006516 5463475 0.04046823191852458 0.3700190050286572 chr12 133851895 6768359 0.05056603046225083 0.2548847655651877 chr13 115169878 2274676 0.019750615694843404 0.1533694624881528 chr14 107349540 4073821 0.03794912395525868 0.2628495465065265 chr15 102531392 3521146 0.034342126165613746 0.2138142801486747 chr16 90354753 3443613 0.03811214004425423 0.25784799793102425 chr17 81195210 3674925 0.04526036696007067 0.2685307749239745 chr18 78077248 3893453 0.04986667819029687 0.788867922833279 chr19 59128983 2388784 0.040399544839118916 0.539576483600272 chr20 63025520 3044244 0.048301767284109676 0.24893426163201463 chr21 48129895 1475046 0.030647189236544147 0.22629233880364805 chr22 51304566 1808771 0.03525555600645759 0.20480377270928643 chrMT 16571 7594 0.45827047251222014 0.850030022771028 chrX 155270560 9077939 0.0584652943867788 0.31285935643311547 chrY 59373566 417405 0.007030148736560644 0.16513160939689545