BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251058.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 1,748,530 number of mapped reads = 1,425,077 (81.5%) number of supplementary alignments = 40,100 (2.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 713,828 number of mapped paired reads (second in pair) = 711,249 number of mapped paired reads (both in pair) = 1,415,314 number of mapped paired reads (singletons) = 9,763 number of mapped bases = 173,086,921 bp number of sequenced bases = 172,934,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 233,513 duplication rate = 14.73% >>>>>>> Insert size mean insert size = 96,563.2724 std insert size = 2,987,141.4621 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 52.9199 >>>>>>> ACTG content number of A's = 50,728,126 bp (29.33%) number of C's = 35,228,415 bp (20.37%) number of T's = 50,709,600 bp (29.32%) number of G's = 36,262,332 bp (20.97%) number of N's = 5,753 bp (0%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,261,146 number of insertions = 30,222 mapped reads with insertion percentage = 1.97% number of deletions = 72,494 mapped reads with deletion percentage = 4.88% homopolymer indels = 42.82% >>>>>>> Coverage mean coverageData = 0.0559X std coverageData = 0.7005X There is a 3.41% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 14799932 0.0593777136466994 1.442079833640091 chr2 243199373 15478163 0.06364392641752412 1.0466479191056173 chr3 198022430 12019775 0.060699058182449334 0.35786959046180056 chr4 191154276 10295486 0.053859564198291854 0.4072975645942387 chr5 180915260 10414529 0.05756578521900253 0.35922826341372943 chr6 171115067 9746787 0.05696042534933525 0.396120651963049 chr7 159138663 9222820 0.05795461534071076 0.9447807262716811 chr8 146364022 8389646 0.05732041170609537 0.4117739238930721 chr9 141213431 7534040 0.05335214891846938 0.8326369433512738 chr10 135534747 10223594 0.07543153491111766 0.8627365249654041 chr11 135006516 7891744 0.05845454155709048 0.450244593080426 chr12 133851895 7530807 0.05626223670572613 0.35595371872387505 chr13 115169878 4952080 0.042998048500146886 0.3086627326775734 chr14 107349540 5017833 0.046742939000949606 0.33014088391534474 chr15 102531392 5198003 0.05069669784645077 0.3257614045647824 chr16 90354753 5050372 0.05589492342478099 0.656355248923824 chr17 81195210 4878655 0.060085502580755686 0.4276113464807865 chr18 78077248 4375485 0.05604046136462187 0.7201636436839833 chr19 59128983 3467853 0.058648953931779955 0.7385376076368844 chr20 63025520 3609592 0.05727191144158747 0.36725033294954845 chr21 48129895 2098858 0.043608198189503636 0.32905109269333577 chr22 51304566 2117239 0.04126804230251163 0.3076507818886909 chrMT 16571 225896 13.632007724337699 8.550309591590766 chrX 155270560 8150527 0.05249241710727391 0.3473285359785665 chrY 59373566 397205 0.00668992999342502 0.5018558009561342