BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818968.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,601,284 number of mapped reads = 1,527,742 (95.41%) number of supplementary alignments = 24,654 (1.54%) number of secondary alignments = 0 number of mapped bases = 141,330,342 bp number of sequenced bases = 141,248,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 669,602 duplication rate = 36.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9223 >>>>>>> ACTG content number of A's = 41,924,393 bp (29.68%) number of C's = 28,932,608 bp (20.48%) number of T's = 40,586,107 bp (28.73%) number of G's = 29,799,020 bp (21.1%) number of N's = 6,710 bp (0%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 879,048 number of insertions = 26,058 mapped reads with insertion percentage = 1.67% number of deletions = 45,357 mapped reads with deletion percentage = 2.9% homopolymer indels = 40.28% >>>>>>> Coverage mean coverageData = 0.0457X std coverageData = 0.5509X There is a 2.17% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 13634638 0.054702523690001156 0.930950718010023 chr2 243199373 10925575 0.044924355129813597 0.7392622488229728 chr3 198022430 8255509 0.04168976716425508 0.3732584262737177 chr4 191154276 8080087 0.042269977784854786 0.40126950541543627 chr5 180915260 8717568 0.048185918645005404 0.4054547975748019 chr6 171115067 6230833 0.03641311726219878 0.3769364680145816 chr7 159138663 4522415 0.02841807838991333 0.46106300337170286 chr8 146364022 11979477 0.08184714273566492 0.58744176365158 chr9 141213431 5506214 0.03899214091044923 0.545363883225897 chr10 135534747 6474418 0.0477694328820343 0.6134264186709825 chr11 135006516 5534534 0.04099456947692806 0.4343183332948523 chr12 133851895 7346038 0.05488183787013251 0.4352915483430376 chr13 115169878 3522895 0.030588683961269805 0.31897289427770886 chr14 107349540 3904748 0.03637414748120951 0.3692721433621037 chr15 102531392 3757474 0.03664705927331992 0.35457836258693753 chr16 90354753 4560564 0.050473980046185286 0.6363145477798396 chr17 81195210 4999981 0.06157975328840211 0.49006677340366905 chr18 78077248 3748137 0.0480054957879663 0.6601656606967397 chr19 59128983 2743678 0.04640157602575373 0.8246937810990693 chr20 63025520 3718663 0.05900249613172569 0.47046812021246376 chr21 48129895 2172007 0.04512802282240591 0.42115219583223096 chr22 51304566 1220530 0.023789890357906934 0.3056755475738114 chrMT 16571 57247 3.4546496892161005 3.870057468467915 chrX 155270560 9243179 0.059529501278284824 0.5179000479238361 chrY 59373566 473933 0.007982222256955225 0.4237647749734291