BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714077.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 680,552 number of mapped reads = 111,750 (16.42%) number of supplementary alignments = 4,016 (0.59%) number of secondary alignments = 0 number of mapped bases = 11,510,873 bp number of sequenced bases = 11,485,036 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,248 duplication rate = 22.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 16.1409 >>>>>>> ACTG content number of A's = 330,168 bp (2.87%) number of C's = 95,242 bp (0.83%) number of T's = 128,123 bp (1.12%) number of G's = 10,931,065 bp (95.18%) number of N's = 438 bp (0%) GC percentage = 96.01% >>>>>>> Mismatches and indels general error rate = 0.0327 number of mismatches = 278,552 number of insertions = 13,431 mapped reads with insertion percentage = 7.72% number of deletions = 5,663 mapped reads with deletion percentage = 4.86% homopolymer indels = 66.89% >>>>>>> Coverage mean coverageData = 0.0037X std coverageData = 14.0617X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 18732 7.515327313868558E-5 0.017378252286772124 chr2 243199373 10972804 0.04511855382127157 50.16821802349206 chr3 198022430 19094 9.642342031657727E-5 0.024414125874960328 chr4 191154276 16690 8.7311674890286E-5 0.022327717420788255 chr5 180915260 13266 7.332714774861999E-5 0.013054176084847149 chr6 171115067 19074 1.1146885154186919E-4 0.043225364527029506 chr7 159138663 28067 1.7636820286720645E-4 0.1245884230349009 chr8 146364022 14453 9.87469447922113E-5 0.030193750222684675 chr9 141213431 8259 5.848593821079243E-5 0.017210895166910996 chr10 135534747 13261 9.784206849923142E-5 0.023915416067078612 chr11 135006516 13361 9.896559363105111E-5 0.05619714774553997 chr12 133851895 38247 2.857411917851443E-4 0.18987749326649594 chr13 115169878 5804 5.039512154384673E-5 0.009944591664904202 chr14 107349540 17041 1.5874311152148392E-4 0.12170692975067558 chr15 102531392 14659 1.4297084740642164E-4 0.05078342242983008 chr16 90354753 8756 9.690691091812292E-5 0.018916547153680473 chr17 81195210 20135 2.4798260882630886E-4 0.24556765100259081 chr18 78077248 7418 9.500847161006495E-5 0.03016578299535388 chr19 59128983 7811 1.3210103748951678E-4 0.04258313519809849 chr20 63025520 7742 1.2283912929238823E-4 0.07379595188803181 chr21 48129895 2287 4.751724473947014E-5 0.009126508964594101 chr22 51304566 2178 4.245236184241379E-5 0.01033306924426046 chrMT 16571 5032 0.30366302576790777 1.3867571032631902 chrX 155270560 232052 0.0014945009536901264 0.18985158794284898 chrY 59373566 4650 7.831768096933912E-5 0.02365949407105728