BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081920.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,126,164 number of mapped reads = 2,924,016 (93.53%) number of supplementary alignments = 24,701 (0.79%) number of secondary alignments = 0 number of mapped bases = 202,012,263 bp number of sequenced bases = 201,938,020 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,232 duplication rate = 3.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3011 >>>>>>> ACTG content number of A's = 58,662,916 bp (29.05%) number of C's = 37,447,272 bp (18.54%) number of T's = 63,828,011 bp (31.61%) number of G's = 41,973,307 bp (20.79%) number of N's = 26,514 bp (0.01%) GC percentage = 39.33% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,534,756 number of insertions = 14,712 mapped reads with insertion percentage = 0.5% number of deletions = 41,909 mapped reads with deletion percentage = 1.42% homopolymer indels = 47.75% >>>>>>> Coverage mean coverageData = 0.0653X std coverageData = 0.6304X There is a 5.36% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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% 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 15856315 0.06361594982746302 1.2993951459132933 chr2 243199373 17494610 0.07193525947124872 0.5853266336548948 chr3 198022430 13922580 0.07030809590610518 0.314915898006245 chr4 191154276 14038029 0.07343821594657919 0.3390382202201022 chr5 180915260 12828108 0.07090672174364948 0.31173194953805433 chr6 171115067 12270412 0.07170854218231992 0.4052466733071722 chr7 159138663 11185803 0.07028966304687378 0.7022444889120498 chr8 146364022 10534371 0.07197377371878999 1.2707253351403125 chr9 141213431 8420320 0.059628322464596165 0.4881561595083999 chr10 135534747 9464299 0.06982931838135943 0.6410134289444266 chr11 135006516 9023397 0.06683675179055802 0.4290434105076576 chr12 133851895 9048723 0.06760250200417409 0.3127619353583871 chr13 115169878 6808958 0.05912099689816464 0.2816531997486318 chr14 107349540 6143467 0.057228629018810886 0.3005259238316315 chr15 102531392 5432155 0.05298040818562182 0.26727165974726586 chr16 90354753 5163612 0.0571482055847134 0.3427200634153359 chr17 81195210 4626638 0.05698166184926426 0.3104905782891816 chr18 78077248 5595666 0.07166833031819975 0.9409511534747248 chr19 59128983 3334366 0.056391397768502126 0.8810614134959042 chr20 63025520 3819017 0.06059477176864229 0.3024826841152698 chr21 48129895 2682266 0.055729728893029996 0.30250703695992304 chr22 51304566 1831432 0.03569725158575555 0.21555289953955625 chrMT 16571 9467 0.5712992577394242 0.8890712939885713 chrX 155270560 11969889 0.0770905250808653 0.3745649580688071 chrY 59373566 508363 0.008562109946369063 0.19528003626793075