BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472814.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,514,610 number of mapped reads = 1,990,488 (79.16%) number of supplementary alignments = 18,568 (0.74%) number of secondary alignments = 0 number of mapped bases = 124,962,936 bp number of sequenced bases = 124,905,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,578 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2241 >>>>>>> ACTG content number of A's = 34,018,061 bp (27.23%) number of C's = 24,298,252 bp (19.45%) number of T's = 37,445,456 bp (29.98%) number of G's = 29,141,443 bp (23.33%) number of N's = 2,746 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,121,146 number of insertions = 9,685 mapped reads with insertion percentage = 0.48% number of deletions = 32,113 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.0404X std coverageData = 0.3366X There is a 3.2% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 9737627 0.03906761379743964 0.40341488031076517 chr2 243199373 11632409 0.0478307524255007 0.44815218086058634 chr3 198022430 7862388 0.03970453246129744 0.252817570274143 chr4 191154276 6296935 0.03294163819803853 0.25007029044552503 chr5 180915260 7383037 0.040809365666555714 0.2590745643075647 chr6 171115067 8633996 0.0504572516691356 0.30895124096462967 chr7 159138663 7144409 0.0448942379263297 0.46236816976521516 chr8 146364022 7373561 0.050378234345049636 0.35389315498896945 chr9 141213431 5463006 0.0386861643493387 0.35384336198885846 chr10 135534747 6050871 0.04464442612638662 0.3180048203664035 chr11 135006516 5022366 0.03720091554692071 0.36639000541643596 chr12 133851895 5089394 0.03802257711779127 0.26130680112298627 chr13 115169878 5249065 0.045576717551094395 0.27243018982507433 chr14 107349540 3483099 0.0324463337243923 0.2699306704143139 chr15 102531392 3194853 0.031159754468173026 0.25486705211753413 chr16 90354753 3592586 0.03976089669571672 0.27178601179649114 chr17 81195210 3227564 0.03975067002105173 0.2748176470217513 chr18 78077248 2564108 0.03284065544933141 0.571581598456104 chr19 59128983 2520536 0.042627758370205694 0.3507948729718505 chr20 63025520 3977164 0.06310402516314026 0.32712206527333665 chr21 48129895 1704757 0.035419919366123695 0.2619089948255252 chr22 51304566 1348927 0.026292533105143116 0.21308882880032545 chrMT 16571 167236 10.092088588497978 7.366266314586626 chrX 155270560 5681418 0.03659043929512459 0.281984939658965 chrY 59373566 561624 0.009459158979940669 0.144094362618248