BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008733.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,172,230 number of mapped reads = 1,824,981 (84.01%) number of supplementary alignments = 14,748 (0.68%) number of secondary alignments = 0 number of mapped bases = 123,685,978 bp number of sequenced bases = 123,623,716 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 189,902 duplication rate = 7.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7798 >>>>>>> ACTG content number of A's = 34,740,411 bp (28.1%) number of C's = 23,210,631 bp (18.78%) number of T's = 38,992,388 bp (31.54%) number of G's = 26,604,638 bp (21.52%) number of N's = 75,648 bp (0.06%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,008,044 number of insertions = 9,753 mapped reads with insertion percentage = 0.53% number of deletions = 36,748 mapped reads with deletion percentage = 1.99% homopolymer indels = 49.11% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.4451X There is a 2.08% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 10218272 0.040995974088265164 0.649028480258753 chr2 243199373 13945535 0.05734198582822827 0.47177647490004027 chr3 198022430 5966537 0.030130611971583218 0.2882012215074116 chr4 191154276 7975955 0.0417252240802607 0.3611774494877364 chr5 180915260 3560617 0.019681131376092873 0.22987872942102888 chr6 171115067 12792161 0.07475765415794741 0.4981515871859292 chr7 159138663 10058255 0.0632043452570668 0.9284648863193683 chr8 146364022 5244308 0.03583058137060486 0.4597279476652027 chr9 141213431 7230098 0.0511997899123349 0.42345073267098493 chr10 135534747 4256665 0.031406448119167554 0.3772190542922791 chr11 135006516 3770293 0.027926748365241866 0.3400251329830073 chr12 133851895 5361824 0.04005788636761549 0.340667777714479 chr13 115169878 2115999 0.018372850928955572 0.22473001813476207 chr14 107349540 3003103 0.02797499644618878 0.28901156035496617 chr15 102531392 3363078 0.03280047148877097 0.3054923428160418 chr16 90354753 2677453 0.029632674664054476 0.29237385864283505 chr17 81195210 2532833 0.031194364790730882 0.331290408188641 chr18 78077248 1872834 0.023986936629733672 0.4763992603246231 chr19 59128983 3044629 0.05149131349003584 0.4514152704025903 chr20 63025520 1984789 0.031491830610838274 0.30167045876384213 chr21 48129895 1800730 0.037413960699477944 0.33578839169142566 chr22 51304566 727494 0.0141799074959527 0.1892277812169863 chrMT 16571 34429 2.077665801701768 2.753653531673958 chrX 155270560 9808179 0.06316831085042779 0.4429662750141686 chrY 59373566 339908 0.005724904581274434 0.16404768846200726