BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716899.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 = 888,199 number of mapped reads = 724,466 (81.57%) number of supplementary alignments = 3,169 (0.36%) number of secondary alignments = 0 number of mapped bases = 40,582,200 bp number of sequenced bases = 40,569,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,360 duplication rate = 1.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4233 >>>>>>> ACTG content number of A's = 9,348,394 bp (23.04%) number of C's = 8,415,259 bp (20.74%) number of T's = 12,209,910 bp (30.1%) number of G's = 10,595,272 bp (26.12%) number of N's = 1,125 bp (0%) GC percentage = 46.86% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 215,634 number of insertions = 2,954 mapped reads with insertion percentage = 0.41% number of deletions = 7,066 mapped reads with deletion percentage = 0.97% homopolymer indels = 34.05% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 0.1379X There is a 1.21% of reference with a coverageData >= 1X There is a 0.07% 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 4031101 0.01617288247398188 0.15895277920033116 chr2 243199373 3453988 0.014202289904752344 0.16007087428494488 chr3 198022430 2680698 0.013537345239122658 0.12788391798600468 chr4 191154276 2574021 0.013465673140369614 0.13841817816960095 chr5 180915260 2438009 0.01347597212087029 0.12310266812840345 chr6 171115067 1739185 0.010163833205874268 0.10999222750852308 chr7 159138663 2263999 0.01422658050105649 0.14998024557914322 chr8 146364022 2485336 0.016980511781782 0.14449943075304214 chr9 141213431 1779230 0.012599580559727354 0.12987285652476882 chr10 135534747 2177280 0.016064367611945296 0.19956594947987638 chr11 135006516 1675877 0.012413304554870523 0.1405509248976667 chr12 133851895 1999005 0.014934454233912788 0.13103231153043662 chr13 115169878 720575 0.006256627275406161 0.0853715294532052 chr14 107349540 1297406 0.012085808658332397 0.11960897735252693 chr15 102531392 830962 0.008104464240571317 0.09682140106335406 chr16 90354753 1137899 0.012593681707037592 0.12687366705000694 chr17 81195210 1630013 0.020075235965274305 0.15881472729793922 chr18 78077248 1093220 0.014001774242862659 0.15587972779045234 chr19 59128983 1099039 0.018587145326007044 0.1737090652810022 chr20 63025520 1036344 0.01644324394308845 0.14132365544506528 chr21 48129895 553433 0.01149873690769531 0.12154901652402075 chr22 51304566 474478 0.00924826067137962 0.11221814121646594 chrMT 16571 6072 0.3664232695673164 0.6904090820702291 chrX 155270560 1272358 0.008194457468305646 0.10280233859419372 chrY 59373566 132672 0.002234529756895518 0.08338227008204784