BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514706.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 74,101,938 number of mapped reads = 72,721,431 (98.14%) number of supplementary alignments = 5,282,425 (7.13%) number of secondary alignments = 0 number of mapped bases = 6,607,049,705 bp number of sequenced bases = 6,599,721,041 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,338,819 duplication rate = 37.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5285 >>>>>>> ACTG content number of A's = 1,944,369,446 bp (29.46%) number of C's = 1,360,924,206 bp (20.62%) number of T's = 1,910,074,041 bp (28.94%) number of G's = 1,377,135,888 bp (20.87%) number of N's = 7,217,460 bp (0.11%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 48,021,841 number of insertions = 3,028,581 mapped reads with insertion percentage = 3.96% number of deletions = 3,238,048 mapped reads with deletion percentage = 4.16% homopolymer indels = 33.48% >>>>>>> Coverage mean coverageData = 2.1343X std coverageData = 381.6511X There is a 8.77% of reference with a coverageData >= 1X There is a 6.53% of reference with a coverageData >= 2X There is a 5.61% of reference with a coverageData >= 3X There is a 5.07% of reference with a coverageData >= 4X There is a 4.67% of reference with a coverageData >= 5X There is a 4.34% of reference with a coverageData >= 6X There is a 4.07% of reference with a coverageData >= 7X There is a 3.83% of reference with a coverageData >= 8X There is a 3.62% of reference with a coverageData >= 9X There is a 3.44% of reference with a coverageData >= 10X There is a 3.27% of reference with a coverageData >= 11X There is a 3.11% of reference with a coverageData >= 12X There is a 2.97% of reference with a coverageData >= 13X There is a 2.85% of reference with a coverageData >= 14X There is a 2.73% of reference with a coverageData >= 15X There is a 2.62% of reference with a coverageData >= 16X There is a 2.51% of reference with a coverageData >= 17X There is a 2.42% of reference with a coverageData >= 18X There is a 2.33% of reference with a coverageData >= 19X There is a 2.24% of reference with a coverageData >= 20X There is a 2.16% of reference with a coverageData >= 21X There is a 2.09% of reference with a coverageData >= 22X There is a 2.01% of reference with a coverageData >= 23X There is a 1.95% of reference with a coverageData >= 24X There is a 1.88% of reference with a coverageData >= 25X There is a 1.82% of reference with a coverageData >= 26X There is a 1.76% of reference with a coverageData >= 27X There is a 1.71% of reference with a coverageData >= 28X There is a 1.66% of reference with a coverageData >= 29X There is a 1.61% of reference with a coverageData >= 30X There is a 1.56% of reference with a coverageData >= 31X There is a 1.51% of reference with a coverageData >= 32X There is a 1.47% of reference with a coverageData >= 33X There is a 1.43% of reference with a coverageData >= 34X There is a 1.39% of reference with a coverageData >= 35X There is a 1.35% of reference with a coverageData >= 36X There is a 1.31% of reference with a coverageData >= 37X There is a 1.27% of reference with a coverageData >= 38X There is a 1.24% of reference with a coverageData >= 39X There is a 1.21% of reference with a coverageData >= 40X There is a 1.18% of reference with a coverageData >= 41X There is a 1.15% of reference with a coverageData >= 42X There is a 1.12% of reference with a coverageData >= 43X There is a 1.09% of reference with a coverageData >= 44X There is a 1.06% of reference with a coverageData >= 45X There is a 1.03% of reference with a coverageData >= 46X There is a 1.01% of reference with a coverageData >= 47X There is a 0.98% of reference with a coverageData >= 48X There is a 0.96% of reference with a coverageData >= 49X There is a 0.94% of reference with a coverageData >= 50X There is a 0.92% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 509592222 2.044497301372822 166.49806554674097 chr2 243199373 346950581 1.426609685379411 15.610001422726514 chr3 198022430 292662928 1.4779281720762643 12.444827490842531 chr4 191154276 470885466 2.463379192208078 20.92255278919235 chr5 180915260 268603902 1.4846945581041644 21.18628294219165 chr6 171115067 412151185 2.4086200720127118 89.10564061368021 chr7 159138663 316129278 1.9865020356492502 18.78714984216243 chr8 146364022 238343676 1.6284307628550956 14.611112280911158 chr9 141213431 812694566 5.755079812486108 1214.474797129903 chr10 135534747 312828986 2.3081091227476893 64.65975121027105 chr11 135006516 377891528 2.7990614023400173 24.170812204583402 chr12 133851895 259928505 1.9419112818686655 17.045642881223785 chr13 115169878 151486843 1.315333884438082 15.143418520105984 chr14 107349540 109428693 1.0193680662255282 10.512761619920465 chr15 102531392 218235334 2.128473336244182 68.42850101186544 chr16 90354753 217336615 2.4053700307276586 29.965895918420593 chr17 81195210 135470383 1.6684528927260611 14.888070147739612 chr18 78077248 191751636 2.455922063236655 19.605411632412356 chr19 59128983 93690470 1.584510087041409 13.675181514881606 chr20 63025520 119410882 1.894643344473794 32.95367778650976 chr21 48129895 399838307 8.307483467395889 2198.140008783841 chr22 51304566 60185388 1.1731000316813907 17.211609888803828 chrMT 16571 3190717 192.5482469374208 122.78178281010102 chrX 155270560 255579533 1.646026993140232 13.903477826484663 chrY 59373566 32782081 0.5521325938212975 4.141921173007326