BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472706.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 9,190,544 number of mapped reads = 9,090,218 (98.91%) number of supplementary alignments = 28,464 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,566,381 number of mapped paired reads (second in pair) = 4,523,837 number of mapped paired reads (both in pair) = 9,029,444 number of mapped paired reads (singletons) = 60,774 number of mapped bases = 888,709,802 bp number of sequenced bases = 888,601,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,073,750 duplication rate = 44.67% >>>>>>> Insert size mean insert size = 17,428.7411 std insert size = 1,309,060.6332 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 55.2118 >>>>>>> ACTG content number of A's = 237,581,331 bp (26.74%) number of C's = 208,308,545 bp (23.44%) number of T's = 235,719,237 bp (26.53%) number of G's = 206,820,192 bp (23.27%) number of N's = 172,185 bp (0.02%) GC percentage = 46.72% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 5,340,256 number of insertions = 49,349 mapped reads with insertion percentage = 0.54% number of deletions = 46,294 mapped reads with deletion percentage = 0.5% homopolymer indels = 43.37% >>>>>>> Coverage mean coverageData = 0.2871X std coverageData = 9.8602X There is a 2.83% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.23% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.18% of reference with a coverageData >= 21X There is a 0.18% of reference with a coverageData >= 22X There is a 0.17% of reference with a coverageData >= 23X There is a 0.17% of reference with a coverageData >= 24X There is a 0.17% of reference with a coverageData >= 25X There is a 0.16% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.15% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 90885068 0.3646332660491145 13.647256801489727 chr2 243199373 57040921 0.2345438653741924 7.188074202636477 chr3 198022430 92361887 0.46642133923919626 11.011333052454447 chr4 191154276 36668548 0.19182698272467627 8.88105551716459 chr5 180915260 46776584 0.2585552152980351 8.719752148487558 chr6 171115067 58548432 0.3421582507401292 10.534800235304218 chr7 159138663 42220578 0.2653068538096239 8.290803672205616 chr8 146364022 38886667 0.26568460246330206 10.738879940335044 chr9 141213431 47171414 0.3340433956313971 8.714311968035549 chr10 135534747 23782230 0.17546961592070556 6.123211518148565 chr11 135006516 36815329 0.2726929787596326 9.146980986897999 chr12 133851895 58801432 0.43930220039096196 13.657859109728204 chr13 115169878 18257823 0.15852949848570647 6.095001109150028 chr14 107349540 26023278 0.24241629726592215 10.26799860455127 chr15 102531392 24360959 0.2375951259883412 8.247881950441318 chr16 90354753 26319874 0.29129484754388074 8.244466760738055 chr17 81195210 35155788 0.432978595658537 10.807830250525596 chr18 78077248 11598998 0.14855797683852792 5.030291868340186 chr19 59128983 18182641 0.30750809632562087 8.418791429546841 chr20 63025520 27097042 0.4299376189200819 18.212977899234918 chr21 48129895 7946395 0.1651031027597297 8.520708481658579 chr22 51304566 8001499 0.15596075795670897 4.269751598222517 chrMT 16571 2748 0.16583187496228352 0.5780098163113815 chrX 155270560 54366877 0.3501428538674685 11.484953553291177 chrY 59373566 1436790 0.024199152868803604 0.9599176357478778