BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708572.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 = 4,272,512 number of mapped reads = 3,488,368 (81.65%) number of supplementary alignments = 90 (0%) number of secondary alignments = 0 number of mapped bases = 173,969,109 bp number of sequenced bases = 173,953,416 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,739 duplication rate = 0.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5771 >>>>>>> ACTG content number of A's = 53,964,379 bp (31.02%) number of C's = 33,009,634 bp (18.98%) number of T's = 53,666,187 bp (30.85%) number of G's = 33,305,883 bp (19.15%) number of N's = 7,333 bp (0%) GC percentage = 38.12% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 272,264 number of insertions = 11,610 mapped reads with insertion percentage = 0.33% number of deletions = 9,455 mapped reads with deletion percentage = 0.27% homopolymer indels = 48.04% >>>>>>> Coverage mean coverageData = 0.0562X std coverageData = 0.2445X There is a 5.31% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 13977687 0.056078845235856004 0.24542060750384198 chr2 243199373 15095525 0.06207057532175463 0.2558166611551192 chr3 198022430 12181116 0.061513819419345576 0.25499103841692733 chr4 191154276 13426635 0.07023978370224897 0.2721994803367708 chr5 180915260 13914194 0.07691000748085043 0.2846839625233087 chr6 171115067 10559299 0.061708762326581096 0.2551563984849323 chr7 159138663 9199141 0.0578058205754814 0.2476717176568749 chr8 146364022 8524518 0.058241894992472946 0.24765261415720136 chr9 141213431 7930212 0.05615763276794825 0.24478751943705113 chr10 135534747 7056425 0.05206358632152093 0.23403280824720757 chr11 135006516 8848044 0.06553790337053064 0.2646411079131432 chr12 133851895 8650047 0.06462401596929203 0.2622147853949766 chr13 115169878 6038637 0.052432433765363544 0.235673468342761 chr14 107349540 5445413 0.050726002179422476 0.2322386130711523 chr15 102531392 4399975 0.042913442548405074 0.21382493166675587 chr16 90354753 3559444 0.039394098061448966 0.20443724256458148 chr17 81195210 2548247 0.03138420357555575 0.18204445127972063 chr18 78077248 4673830 0.05986161295029251 0.2511249699719075 chr19 59128983 1383574 0.02339925244443998 0.15651003322222676 chr20 63025520 2640312 0.04189274439941154 0.2107362575576987 chr21 48129895 2302986 0.04784938757917506 0.22790057561781243 chr22 51304566 1044058 0.0203501965107745 0.14661464370456387 chrMT 16571 0 0.0 0.0 chrX 155270560 10343958 0.06661892634379628 0.2668334296073072 chrY 59373566 225832 0.0038035781782081272 0.06410114614615182