BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472495.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 = 15,436,628 number of mapped reads = 15,279,379 (98.98%) number of supplementary alignments = 51,557 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,664,915 number of mapped paired reads (second in pair) = 7,614,464 number of mapped paired reads (both in pair) = 15,192,878 number of mapped paired reads (singletons) = 86,501 number of mapped bases = 1,504,885,308 bp number of sequenced bases = 1,504,681,152 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,416,685 duplication rate = 44.72% >>>>>>> Insert size mean insert size = 26,235.5998 std insert size = 1,655,760.1906 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 55.1756 >>>>>>> ACTG content number of A's = 409,707,628 bp (27.23%) number of C's = 345,147,257 bp (22.94%) number of T's = 406,967,624 bp (27.05%) number of G's = 342,626,301 bp (22.77%) number of N's = 232,342 bp (0.02%) GC percentage = 45.71% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 9,191,630 number of insertions = 79,084 mapped reads with insertion percentage = 0.51% number of deletions = 75,632 mapped reads with deletion percentage = 0.49% homopolymer indels = 44.29% >>>>>>> Coverage mean coverageData = 0.4861X std coverageData = 18.8035X There is a 4.89% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 239069795 0.9591542602415422 43.58756918386184 chr2 243199373 88639743 0.3644735671255205 13.173460140516926 chr3 198022430 155105022 0.7832699659326471 17.969757111153406 chr4 191154276 53144341 0.27801806013484104 10.994350063148145 chr5 180915260 70046476 0.38717837290231905 11.295193159508685 chr6 171115067 102675881 0.6000399777770592 17.23873378401097 chr7 159138663 76995390 0.48382579411264753 21.110175953278574 chr8 146364022 72062167 0.4923489120844192 15.617202919803125 chr9 141213431 72488669 0.5133270149069602 12.910424840580792 chr10 135534747 36093924 0.2663075321932021 9.477767308510604 chr11 135006516 51958280 0.3848575723559891 13.813867607163107 chr12 133851895 67525248 0.5044773404216653 17.238468116144524 chr13 115169878 27395483 0.2378702094309764 8.372200810598406 chr14 107349540 60875393 0.5670764215664083 22.68293263099721 chr15 102531392 43350528 0.422802491553026 14.951266023967754 chr16 90354753 45097915 0.4991205609294289 14.406731135018655 chr17 81195210 47939025 0.5904169100615665 15.108388778232579 chr18 78077248 27907016 0.3574282741113006 11.801563718573528 chr19 59128983 34835670 0.5891471192731321 19.07662689387304 chr20 63025520 37567547 0.5960688146642821 15.249625695255016 chr21 48129895 12443575 0.2585414948443166 13.400435620866292 chr22 51304566 15848074 0.3089018236700414 10.544334947900731 chrMT 16571 2070 0.12491702371613059 0.37701617487872646 chrX 155270560 63551891 0.40929775097095034 12.650106171405218 chrY 59373566 2266185 0.03816824813924769 1.0602924403236835