BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081247.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,791,190 number of mapped reads = 3,123,012 (82.38%) number of supplementary alignments = 26,469 (0.7%) number of secondary alignments = 0 number of mapped bases = 210,553,393 bp number of sequenced bases = 210,462,474 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 199,199 duplication rate = 5.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1051 >>>>>>> ACTG content number of A's = 58,561,344 bp (27.83%) number of C's = 37,985,854 bp (18.05%) number of T's = 67,899,248 bp (32.26%) number of G's = 45,960,334 bp (21.84%) number of N's = 55,694 bp (0.03%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,808,806 number of insertions = 17,255 mapped reads with insertion percentage = 0.55% number of deletions = 53,910 mapped reads with deletion percentage = 1.71% homopolymer indels = 49.69% >>>>>>> Coverage mean coverageData = 0.068X std coverageData = 0.5588X There is a 5.13% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 20859097 0.08368724184643055 1.0859367291228548 chr2 243199373 14298308 0.05879253644292907 0.5146374228212831 chr3 198022430 10808975 0.05458459933048999 0.29626508374893495 chr4 191154276 7583031 0.039669690674353525 0.283780979708418 chr5 180915260 14841287 0.08203446740755865 0.3631801490827719 chr6 171115067 11803983 0.06898272143387583 0.3871502078571538 chr7 159138663 16926957 0.10636608779351124 0.9550629548604659 chr8 146364022 12346605 0.08435546407709403 0.8180002953922823 chr9 141213431 9716128 0.0688045600988195 0.48210524699769736 chr10 135534747 5354631 0.039507440848360456 0.3874897549774523 chr11 135006516 10305835 0.07633583404226207 0.47474972823777445 chr12 133851895 5799845 0.04333031669069758 0.2666918731882746 chr13 115169878 6573865 0.05707972530803584 0.2991602408370369 chr14 107349540 7497931 0.06984595369481789 0.34840791474853716 chr15 102531392 7474045 0.07289518706622065 0.33893471837500266 chr16 90354753 6965094 0.0770860831195012 0.3718995065697986 chr17 81195210 3143082 0.03871018992376521 0.2802342728198832 chr18 78077248 7493850 0.09597994539971491 0.7688658527687776 chr19 59128983 4977704 0.08418382572215051 0.7980403957253793 chr20 63025520 5316530 0.08435519453072343 0.3734467071320709 chr21 48129895 3099266 0.0643937826999207 0.3603053404005876 chr22 51304566 1743994 0.03399295883333269 0.22509177058872037 chrMT 16571 99213 5.987146219298775 4.141709205921852 chrX 155270560 14920575 0.09609403740155249 0.43151603768591984 chrY 59373566 603562 0.010165500249723926 0.23554182277538177