BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524448.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 = 3,826,606 number of mapped reads = 3,530,264 (92.26%) number of supplementary alignments = 7,919 (0.21%) number of secondary alignments = 0 number of mapped bases = 206,289,657 bp number of sequenced bases = 206,224,118 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 280,218 duplication rate = 5.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4496 >>>>>>> ACTG content number of A's = 51,063,630 bp (24.76%) number of C's = 41,860,090 bp (20.3%) number of T's = 65,983,676 bp (32%) number of G's = 47,312,372 bp (22.94%) number of N's = 4,350 bp (0%) GC percentage = 43.24% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 963,250 number of insertions = 13,102 mapped reads with insertion percentage = 0.37% number of deletions = 38,445 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 0.0666X std coverageData = 0.5358X There is a 5.22% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 20251176 0.081248246920115 0.9898546527720193 chr2 243199373 15934042 0.0655184337173435 0.6303353636072823 chr3 198022430 11279360 0.05696001205520001 0.2973400538016763 chr4 191154276 11692274 0.061166688209475364 0.38129881776931374 chr5 180915260 11110018 0.06141006568489579 0.3073042067391218 chr6 171115067 8807350 0.05147033604001686 0.40039686565654337 chr7 159138663 10266757 0.0645145359804864 0.7683725571572356 chr8 146364022 19104491 0.13052723434998253 0.5562122910800319 chr9 141213431 8789319 0.06224138127484488 0.4711184569882113 chr10 135534747 10710955 0.07902737295846356 0.551235557720475 chr11 135006516 7116377 0.05271135950208507 0.5329148927655253 chr12 133851895 9480798 0.07083051009475809 0.3319669377399824 chr13 115169878 4489774 0.038983925988008775 0.24921186283451807 chr14 107349540 4899476 0.045640400508469806 0.2777237545003054 chr15 102531392 5444277 0.05309863539158817 0.3067028195467239 chr16 90354753 6443819 0.07131687914635769 0.3659892673095543 chr17 81195210 7177559 0.08839879840202396 0.4048256069552122 chr18 78077248 4868704 0.06235752571607032 0.8723649061631596 chr19 59128983 4192702 0.07090773064708385 0.7216559030260132 chr20 63025520 6648423 0.1054877928813598 0.4197875293050903 chr21 48129895 2848446 0.05918246860916692 0.33997429490208847 chr22 51304566 1711514 0.03335987677977824 0.22080651608890775 chrMT 16571 56966 3.4376923541126065 2.769675029570482 chrX 155270560 12331575 0.07941991707893628 0.42118689728483877 chrY 59373566 633505 0.01066981558763036 0.26099247640769885