BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716415.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 = 2,232,030 number of mapped reads = 2,056,492 (92.14%) number of supplementary alignments = 14,153 (0.63%) number of secondary alignments = 0 number of mapped bases = 121,109,077 bp number of sequenced bases = 121,074,670 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,631 duplication rate = 5.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8928 >>>>>>> ACTG content number of A's = 30,079,776 bp (24.84%) number of C's = 22,869,898 bp (18.89%) number of T's = 36,573,164 bp (30.21%) number of G's = 31,550,375 bp (26.06%) number of N's = 1,457 bp (0%) GC percentage = 44.95% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 610,382 number of insertions = 8,460 mapped reads with insertion percentage = 0.41% number of deletions = 21,312 mapped reads with deletion percentage = 1.03% homopolymer indels = 41.58% >>>>>>> Coverage mean coverageData = 0.0391X std coverageData = 0.3354X There is a 3.19% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 10601012 0.04253153696254983 0.5243528933756584 chr2 243199373 9044307 0.037188858213051394 0.43210132966738685 chr3 198022430 8180770 0.041312340223276726 0.24057950251884025 chr4 191154276 4952432 0.025908036710620065 0.25467602266737316 chr5 180915260 4453960 0.0246190398753538 0.18697677113558117 chr6 171115067 7415086 0.04333391635232215 0.2696439311032597 chr7 159138663 7140866 0.044871974323423845 0.4523837147937928 chr8 146364022 6702531 0.04579356940601154 0.3584684368105869 chr9 141213431 5501473 0.038958567616702126 0.28401586803524637 chr10 135534747 6351426 0.04686197554934013 0.3743588947590821 chr11 135006516 5998951 0.04443452936745661 0.3268198103887572 chr12 133851895 4801094 0.035868703988090715 0.22852682408933925 chr13 115169878 3991606 0.03465841997331976 0.2241332279661162 chr14 107349540 3975164 0.037030098126177344 0.23589164519115935 chr15 102531392 3620771 0.035313779803165066 0.22649330750841273 chr16 90354753 3674658 0.04066922743953492 0.25529526674320746 chr17 81195210 3744922 0.04612244983417125 0.2782194044268904 chr18 78077248 3368050 0.04313740668728488 0.5439932384252505 chr19 59128983 2857179 0.04832112536080656 0.4001759655021773 chr20 63025520 2881080 0.04571291121437792 0.26317397693308886 chr21 48129895 1734895 0.03604609983046919 0.2656508412053197 chr22 51304566 2512682 0.04897579681309457 0.26795590617759146 chrMT 16571 29051 1.7531229255929033 1.910732637970989 chrX 155270560 7143687 0.04600799404600589 0.2787441222019704 chrY 59373566 431424 0.007266263912799174 0.22037175654955307