BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716315.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 = 1,730,035 number of mapped reads = 1,596,705 (92.29%) number of supplementary alignments = 33,184 (1.92%) number of secondary alignments = 0 number of mapped bases = 125,500,795 bp number of sequenced bases = 125,444,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,969 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1331 >>>>>>> ACTG content number of A's = 32,813,379 bp (26.16%) number of C's = 25,231,257 bp (20.11%) number of T's = 37,817,270 bp (30.15%) number of G's = 29,574,233 bp (23.58%) number of N's = 8,720 bp (0.01%) GC percentage = 43.69% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 832,077 number of insertions = 9,700 mapped reads with insertion percentage = 0.6% number of deletions = 29,015 mapped reads with deletion percentage = 1.79% homopolymer indels = 42.83% >>>>>>> Coverage mean coverageData = 0.0405X std coverageData = 0.3835X There is a 3.49% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 12498026 0.050142406666260624 0.807918863412244 chr2 243199373 10576090 0.043487324286810555 0.4011993177369549 chr3 198022430 8254439 0.04168436373596668 0.22710086076118982 chr4 191154276 7911901 0.041390133485687756 0.2904590521529767 chr5 180915260 7519755 0.041565067534933206 0.2292466651341722 chr6 171115067 7120617 0.04161303340985163 0.2454006634499833 chr7 159138663 6740011 0.042353070416332454 0.4468502387077297 chr8 146364022 3454856 0.02360454401833806 0.3948142869665634 chr9 141213431 5194228 0.036782818484170955 0.3082462118194004 chr10 135534747 6041071 0.04457211994500569 0.3979951394140765 chr11 135006516 6999101 0.05184269031873987 0.38554831575407555 chr12 133851895 5382420 0.04021175792841782 0.22577690153659327 chr13 115169878 4395274 0.03816339894012912 0.21997571614685546 chr14 107349540 3728138 0.03472896111152409 0.2211054263103576 chr15 102531392 3618449 0.035291133080491095 0.20753296254273362 chr16 90354753 2945079 0.03259462177933241 0.22283756699859675 chr17 81195210 4077713 0.050221102944373194 0.2972403323120586 chr18 78077248 3286874 0.04209771840318962 0.5256626315110312 chr19 59128983 2506597 0.042392019494060976 0.56905444615567 chr20 63025520 2674797 0.04243990370884683 0.24035986474588497 chr21 48129895 1713042 0.03559205770135173 0.24214345025428896 chr22 51304566 1496383 0.02916666325566422 0.19292031886145872 chrMT 16571 12400 0.7482952145314103 1.0279457343200713 chrX 155270560 6958612 0.04481604239721941 0.27422552180806914 chrY 59373566 394922 0.0066514785384458805 0.2255599176327578