BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708544.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 23,565,000 number of mapped reads = 22,720,707 (96.42%) number of supplementary alignments = 560 (0%) number of secondary alignments = 0 number of mapped bases = 1,133,082,635 bp number of sequenced bases = 1,132,986,421 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,372 duplication rate = 0.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5862 >>>>>>> ACTG content number of A's = 353,216,529 bp (31.18%) number of C's = 211,421,611 bp (18.66%) number of T's = 352,945,529 bp (31.15%) number of G's = 214,922,843 bp (18.97%) number of N's = 479,909 bp (0.04%) GC percentage = 37.63% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,964,984 number of insertions = 63,176 mapped reads with insertion percentage = 0.28% number of deletions = 58,613 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.366X std coverageData = 0.6762X There is a 27.84% of reference with a coverageData >= 1X There is a 6.87% of reference with a coverageData >= 2X There is a 1.5% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 88652437 0.3556758921776167 0.6806922636322623 chr2 243199373 103033785 0.42365974767541853 0.7118076623788262 chr3 198022430 88012614 0.44445780207827973 0.7257789294389386 chr4 191154276 95603679 0.5001388459654441 0.7670491808337904 chr5 180915260 80387950 0.4443403502833315 0.7255300532380996 chr6 171115067 76562961 0.44743553178750767 0.7319505946410233 chr7 159138663 64741762 0.40682610234069894 0.7090149786693576 chr8 146364022 64198057 0.4386191095513896 0.7249131173616086 chr9 141213431 47069901 0.3333245334149554 0.6518673505057501 chr10 135534747 48895760 0.36076180523655677 0.6590605119720803 chr11 135006516 51198668 0.3792310883720605 0.6881189310651898 chr12 133851895 52874238 0.3950204664640721 0.7007004637589811 chr13 115169878 48061643 0.41731087880461243 0.7234450931067573 chr14 107349540 37162537 0.3461825453560397 0.6698445658705795 chr15 102531392 29621423 0.2889010128722333 0.6098320284305108 chr16 90354753 20553775 0.2274786252805096 0.5348352021675958 chr17 81195210 17312075 0.21321547170085525 0.5224606208360757 chr18 78077248 33931208 0.43458509193356815 0.7224103555194222 chr19 59128983 7558900 0.12783747692734712 0.39068857352875824 chr20 63025520 16894910 0.2680645871704034 0.5792606870016005 chr21 48129895 14990625 0.31146182637630937 0.654413990323002 chr22 51304566 5618396 0.10951064277592759 0.36927290050899453 chrMT 16571 511 0.030837004405286344 0.19268536570490802 chrX 155270560 35003043 0.22543258039386216 0.5003643599404389 chrY 59373566 5141777 0.08660044101107217 0.33100897671382806