BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716829.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 = 665,919 number of mapped reads = 473,436 (71.1%) number of supplementary alignments = 478 (0.07%) number of secondary alignments = 0 number of mapped bases = 24,553,401 bp number of sequenced bases = 24,547,126 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,838 duplication rate = 4.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0381 >>>>>>> ACTG content number of A's = 5,200,348 bp (21.19%) number of C's = 4,224,569 bp (17.21%) number of T's = 8,286,580 bp (33.76%) number of G's = 6,835,238 bp (27.85%) number of N's = 391 bp (0%) GC percentage = 45.06% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 176,142 number of insertions = 1,535 mapped reads with insertion percentage = 0.32% number of deletions = 3,659 mapped reads with deletion percentage = 0.77% homopolymer indels = 39.6% >>>>>>> Coverage mean coverageData = 0.0079X std coverageData = 0.1045X There is a 0.73% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 2356025 0.009452433821619245 0.1151707419501204 chr2 243199373 2104471 0.008653274776329297 0.14958887342355956 chr3 198022430 1649054 0.008327612180094953 0.09816029519901286 chr4 191154276 1563699 0.0081802983052286 0.10018871186921628 chr5 180915260 1462652 0.008084735361737866 0.09676592601361626 chr6 171115067 1029786 0.006018090738906119 0.08968945596318406 chr7 159138663 1368513 0.008599500424356336 0.10683011744983648 chr8 146364022 1492330 0.010196016613973617 0.11011653185724646 chr9 141213431 1072945 0.007598037894851518 0.09769383743871318 chr10 135534747 1231069 0.009083050857799587 0.11298696731848736 chr11 135006516 1070512 0.007929335795910769 0.10207821348571833 chr12 133851895 1135713 0.008484848122620901 0.09958622899954453 chr13 115169878 414769 0.0036013670171639845 0.06572520791403319 chr14 107349540 1110213 0.01034203779541114 0.11111093034365488 chr15 102531392 493701 0.0048151204267274554 0.07503223083299251 chr16 90354753 628183 0.006952406809191322 0.09249386615473133 chr17 81195210 939607 0.01157219742396134 0.11796684673617602 chr18 78077248 626433 0.008023246413603103 0.10456447724697435 chr19 59128983 675530 0.01142468491298083 0.1269254507577725 chr20 63025520 632921 0.010042297152010805 0.10991867112452941 chr21 48129895 343065 0.0071278983675322795 0.09519828676760976 chr22 51304566 278691 0.00543208961167316 0.0811482874949548 chrMT 16571 2249 0.13571902721622112 0.40138616163334834 chrX 155270560 798127 0.005140233924576559 0.0796325231996409 chrY 59373566 73143 0.0012319118578796497 0.045068908798083236