BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237572.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 = 1,979,267 number of mapped reads = 1,671,244 (84.44%) number of supplementary alignments = 12,690 (0.64%) number of secondary alignments = 0 number of mapped bases = 107,395,732 bp number of sequenced bases = 107,335,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,416 duplication rate = 3.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6422 >>>>>>> ACTG content number of A's = 29,942,515 bp (27.9%) number of C's = 18,491,477 bp (17.23%) number of T's = 34,868,012 bp (32.49%) number of G's = 23,850,897 bp (22.22%) number of N's = 182,349 bp (0.17%) GC percentage = 39.45% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,001,136 number of insertions = 9,573 mapped reads with insertion percentage = 0.57% number of deletions = 36,952 mapped reads with deletion percentage = 2.18% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.0347X std coverageData = 0.4091X There is a 2.96% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.06% 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% 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 8518346 0.03417582658700778 0.6302162510078947 chr2 243199373 10366611 0.042625977493782434 0.40684931902820903 chr3 198022430 7681854 0.03879284786071962 0.2254769366863956 chr4 191154276 8210712 0.04295332634881785 0.25520855049066354 chr5 180915260 5987447 0.03309531213674292 0.21057754838745876 chr6 171115067 5624843 0.03287169913564654 0.23382465586180173 chr7 159138663 6233411 0.039169683108371975 0.43926166073144374 chr8 146364022 6498149 0.044397174327445034 1.055943393663837 chr9 141213431 5051388 0.03577129996933507 0.36381248420835993 chr10 135534747 4653989 0.03433797681416707 0.31529808061085934 chr11 135006516 5023124 0.037206530090740215 0.3103861499182607 chr12 133851895 4399773 0.0328704573065626 0.22005297511956454 chr13 115169878 3536889 0.03071019142696322 0.2003370024909104 chr14 107349540 3056232 0.02846991240018355 0.227182616216889 chr15 102531392 2507505 0.02445597344469877 0.18548249691917515 chr16 90354753 2458664 0.0272112303820918 0.21825073311439908 chr17 81195210 2579115 0.03176437378510383 0.23191367179822592 chr18 78077248 3114778 0.03989354235436167 0.7352354066312838 chr19 59128983 1563119 0.026435749791265648 0.4280247586541807 chr20 63025520 1586226 0.025167995440577087 0.19731628744036767 chr21 48129895 1543642 0.03207241569922394 0.23275643547581817 chr22 51304566 801920 0.015630577598103063 0.14180896655086078 chrMT 16571 38921 2.3487417778045985 2.225617671378904 chrX 155270560 6046105 0.03893915884633893 0.2563734164255735 chrY 59373566 312969 0.005271184149525396 0.15321906036882685