BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234107.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 = 6,535,940 number of mapped reads = 6,098,091 (93.3%) number of supplementary alignments = 41,438 (0.63%) number of secondary alignments = 0 number of mapped bases = 410,986,167 bp number of sequenced bases = 410,831,553 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 623,443 duplication rate = 4.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9252 >>>>>>> ACTG content number of A's = 109,697,993 bp (26.7%) number of C's = 76,442,416 bp (18.61%) number of T's = 119,380,946 bp (29.06%) number of G's = 105,221,748 bp (25.61%) number of N's = 88,450 bp (0.02%) GC percentage = 44.22% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 2,820,712 number of insertions = 29,039 mapped reads with insertion percentage = 0.47% number of deletions = 94,946 mapped reads with deletion percentage = 1.54% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.1328X std coverageData = 32.4917X There is a 8.5% of reference with a coverageData >= 1X There is a 2.5% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 42046251 0.16869065694323787 2.2544483574542764 chr2 243199373 25350342 0.10423687235410758 115.8154740031234 chr3 198022430 27904302 0.14091485494850256 0.5166633292856909 chr4 191154276 11987310 0.06271013262606796 0.3967292476775196 chr5 180915260 24194186 0.13373214619927584 0.5302694994141578 chr6 171115067 37785321 0.2208181994867816 1.0690073140357017 chr7 159138663 46628641 0.29300636389033885 4.263988744715776 chr8 146364022 25909529 0.1770211602958 1.2866626901711187 chr9 141213431 9053628 0.06411308000865724 0.9565764702214077 chr10 135534747 10701051 0.07895429944617818 0.7399557927762143 chr11 135006516 12539873 0.09288346497290545 0.9812088228493856 chr12 133851895 14691169 0.10975689959413723 0.48672293169570124 chr13 115169878 18531750 0.16090795893697135 0.5590574460375356 chr14 107349540 14485654 0.13493913434561527 0.7599545053053754 chr15 102531392 8175241 0.07973402916445337 0.4070280947373774 chr16 90354753 12411011 0.13735869545235765 0.7122573257009575 chr17 81195210 10504158 0.12936918323137536 0.6692119258822857 chr18 78077248 8918128 0.11422185372107378 2.5674404928571706 chr19 59128983 11249909 0.19026048528519424 1.4643785360692303 chr20 63025520 6739469 0.10693238231116538 0.5072838188745442 chr21 48129895 10029207 0.20837791148308135 0.737828357584465 chr22 51304566 4085042 0.07962336139828179 0.38530418104360153 chrMT 16571 12078 0.7288636775089011 1.1400415702386015 chrX 155270560 16101671 0.10370073373857865 0.6549465716952747 chrY 59373566 951246 0.01602137220459354 0.3028783235898019