BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013163.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 = 2,326,647 number of mapped reads = 1,620,947 (69.67%) number of supplementary alignments = 13,306 (0.57%) number of secondary alignments = 0 number of mapped bases = 102,339,167 bp number of sequenced bases = 102,286,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 457,467 duplication rate = 16.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3144 >>>>>>> ACTG content number of A's = 27,018,392 bp (26.41%) number of C's = 18,786,535 bp (18.37%) number of T's = 32,320,229 bp (31.6%) number of G's = 24,004,652 bp (23.47%) number of N's = 156,773 bp (0.15%) GC percentage = 41.83% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 938,782 number of insertions = 7,060 mapped reads with insertion percentage = 0.43% number of deletions = 29,967 mapped reads with deletion percentage = 1.82% homopolymer indels = 45.08% >>>>>>> Coverage mean coverageData = 0.0331X std coverageData = 0.5379X There is a 1% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 8087647 0.03244785095239542 0.6358003010262507 chr2 243199373 9356555 0.03847277599683614 0.6266021253452864 chr3 198022430 6542980 0.033041610488266406 0.5026633694072223 chr4 191154276 6331108 0.033120410029436116 0.4934038188840138 chr5 180915260 5466376 0.030215118392997915 0.4740655325437552 chr6 171115067 5706361 0.03334809201810382 0.5307111091025775 chr7 159138663 7709411 0.04844461336212181 0.7016058979668591 chr8 146364022 5452971 0.03725622544042961 0.5560323048381954 chr9 141213431 3719306 0.026338188752031668 0.47234884175699293 chr10 135534747 4866809 0.03590820145921695 0.5768831738713428 chr11 135006516 4322279 0.03201533620792051 0.527067722600951 chr12 133851895 4996888 0.03733146998030921 0.5379465762230162 chr13 115169878 3165765 0.02748778634635699 0.47631527829378223 chr14 107349540 2967470 0.02764306209416454 0.4667831214381082 chr15 102531392 3093863 0.030174787834734557 0.4661727702088421 chr16 90354753 2747303 0.030405738589092263 0.4697102254503868 chr17 81195210 2419567 0.02979938102259973 0.4901622911681761 chr18 78077248 2473386 0.031678703634636304 0.6347008417565119 chr19 59128983 2150445 0.03636871278506515 0.5497153320116832 chr20 63025520 2611013 0.04142786921869109 0.5678498546448197 chr21 48129895 1537980 0.031954775716838774 0.4726080111715323 chr22 51304566 1099889 0.02143842323897643 0.40592559024806046 chrMT 16571 50955 3.0749502142296783 5.396955005579116 chrX 155270560 4962224 0.03195856316870371 0.4666964841854858 chrY 59373566 500616 0.00843163100562294 0.22160973547447585