BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716226.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 = 3,579,459 number of mapped reads = 3,237,679 (90.45%) number of supplementary alignments = 13,463 (0.38%) number of secondary alignments = 0 number of mapped bases = 185,815,886 bp number of sequenced bases = 185,761,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,388 duplication rate = 3.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5699 >>>>>>> ACTG content number of A's = 47,911,612 bp (25.79%) number of C's = 37,640,430 bp (20.26%) number of T's = 56,269,725 bp (30.29%) number of G's = 43,936,984 bp (23.65%) number of N's = 2,748 bp (0%) GC percentage = 43.92% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,010,766 number of insertions = 13,513 mapped reads with insertion percentage = 0.42% number of deletions = 32,567 mapped reads with deletion percentage = 1% homopolymer indels = 42.25% >>>>>>> Coverage mean coverageData = 0.06X std coverageData = 0.4882X There is a 5.02% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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% 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 14760664 0.059220169405315146 0.870417803012651 chr2 243199373 15795611 0.06494922583538075 0.5680743525324108 chr3 198022430 12435535 0.06279861831813699 0.2938721400141994 chr4 191154276 12163651 0.06363263880113254 0.3544843933834917 chr5 180915260 11243428 0.062147482749658596 0.29634697058077636 chr6 171115067 10735501 0.06273849046852198 0.3482703496898342 chr7 159138663 10208239 0.06414681892859687 0.5885232686871523 chr8 146364022 9410519 0.06429530202442783 0.5099744226768883 chr9 141213431 7778184 0.05508104962055628 0.5172788067979635 chr10 135534747 8854693 0.06533153450310421 0.5024813380024443 chr11 135006516 8523948 0.06313730812814991 0.4651537622566846 chr12 133851895 8477081 0.06333179668468646 0.30689003952831867 chr13 115169878 5890542 0.05114655066318643 0.2594662073994835 chr14 107349540 5635121 0.052493201181858816 0.3147437090062224 chr15 102531392 5270208 0.05140092119299424 0.26580001909641715 chr16 90354753 5416060 0.059942170391412614 0.33309531282973104 chr17 81195210 4914903 0.06053193285663033 0.3220516654996876 chr18 78077248 5027592 0.0643925359664316 0.9717815321053151 chr19 59128983 3692042 0.06244047863972225 0.6638906223203895 chr20 63025520 3870149 0.06140606217925691 0.31303960123351815 chr21 48129895 2438421 0.050663335126743994 0.320971316645002 chr22 51304566 2089768 0.04073259288461772 0.23320862997953473 chrMT 16571 3053 0.18423752338422544 0.44777477977326874 chrX 155270560 10598726 0.06825972676339932 0.3978273223903154 chrY 59373566 582247 0.009806502105667697 0.22853659716267477