BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504708.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,271,932 number of mapped reads = 2,050,418 (90.25%) number of secondary alignments = 0 number of mapped bases = 65,606,356 bp number of sequenced bases = 65,606,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 477,373 duplication rate = 13.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 6.3085 >>>>>>> ACTG content number of A's = 19,039,834 bp (29.02%) number of C's = 12,979,111 bp (19.78%) number of T's = 20,383,792 bp (31.07%) number of G's = 13,203,519 bp (20.13%) number of N's = 100 bp (0%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 31,754 >>>>>>> Coverage mean coverageData = 0.0212X std coverageData = 0.9024X There is a 0.8% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 3751212 0.015049960497390295 1.1265450476611485 chr2 243199373 4259118 0.017512865874041543 0.31584589837920923 chr3 198022430 1731802 0.008745484034308639 0.22738443440251688 chr4 191154276 4571924 0.023917456076159135 0.4354575429000121 chr5 180915260 2194618 0.012130640610416169 0.5006816937680485 chr6 171115067 6113668 0.035728402572521564 1.0453223203664783 chr7 159138663 2051086 0.012888671811953077 0.30752181404525264 chr8 146364022 4819112 0.03292552318629233 2.039677196549001 chr9 141213431 4083994 0.028920719304667275 0.5784736651549756 chr10 135534747 6385748 0.04711520950417239 1.8884781709433731 chr11 135006516 5807504 0.04301647188643843 1.072814437036059 chr12 133851895 2677066 0.020000209933523916 0.9687185803222361 chr13 115169878 1493622 0.012968859791620166 0.6829876952401903 chr14 107349540 611640 0.00569764900715923 0.1864787345919974 chr15 102531392 2917820 0.02845782099593459 1.5039333933221073 chr16 90354753 2227064 0.024648000531859126 0.5550633156967602 chr17 81195210 2099698 0.025859875231556147 0.47763063128519234 chr18 78077248 1701134 0.021787832480980887 0.46209746027880394 chr19 59128983 1790050 0.03027364769659576 0.6494429517110721 chr20 63025520 937494 0.014874831655494473 0.2825531980237731 chr21 48129895 898190 0.018661790141033967 0.28032157847714634 chr22 51304566 1100566 0.021451618945572994 1.2054358875631699 chrMT 16571 0 0.0 0.0 chrX 155270560 777954 0.005010312321923744 0.09576782316905652 chrY 59373566 604272 0.010177458433269782 0.23896252717172997