BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716385.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 = 1,038,290 number of mapped reads = 940,379 (90.57%) number of supplementary alignments = 2,845 (0.27%) number of secondary alignments = 0 number of mapped bases = 53,397,383 bp number of sequenced bases = 53,381,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,983 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1063 >>>>>>> ACTG content number of A's = 13,105,032 bp (24.55%) number of C's = 9,834,515 bp (18.42%) number of T's = 17,346,128 bp (32.49%) number of G's = 13,094,668 bp (24.53%) number of N's = 967 bp (0%) GC percentage = 42.95% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 280,285 number of insertions = 3,766 mapped reads with insertion percentage = 0.4% number of deletions = 10,061 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.21% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 0.1858X There is a 1.61% of reference with a coverageData >= 1X There is a 0.08% 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 4332487 0.017382050975913114 0.2699442946982026 chr2 243199373 4196958 0.01725727310982829 0.24782067875705743 chr3 198022430 3033366 0.015318295003247865 0.13426609242277554 chr4 191154276 3155356 0.0165068554364957 0.14669801314515132 chr5 180915260 3124290 0.017269355829906224 0.13913725538085364 chr6 171115067 2724094 0.015919661826155847 0.15960312205004987 chr7 159138663 3098868 0.019472753770716295 0.2682334245586507 chr8 146364022 2786460 0.01903787530517575 0.1910399564303776 chr9 141213431 1824603 0.01292088852369857 0.14511402486393077 chr10 135534747 2348630 0.017328619058845477 0.20464557739288705 chr11 135006516 1918529 0.014210640025700685 0.1549416517925134 chr12 133851895 2693194 0.020120701316929432 0.1501543345895579 chr13 115169878 1651642 0.014340919940889405 0.126586146179457 chr14 107349540 1820048 0.016954408933657284 0.1396880557002854 chr15 102531392 1962443 0.019139923507524408 0.14839942003988543 chr16 90354753 1879990 0.020806763757076508 0.15903104715238123 chr17 81195210 2404358 0.02961206701725385 0.18767709768422913 chr18 78077248 964547 0.01235375252980228 0.2163678068383183 chr19 59128983 1416856 0.023962123617110073 0.237238287579818 chr20 63025520 1708185 0.027103068725176722 0.1778603799513513 chr21 48129895 688505 0.014305142365259678 0.1368097339972171 chr22 51304566 511845 0.009976597404605275 0.10643034320691273 chrMT 16571 11201 0.6759398949972845 0.9234079435272889 chrX 155270560 2953598 0.019022266680818307 0.15688500003667274 chrY 59373566 187330 0.0031551077797819993 0.11830633330267817