BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472733.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 = 18,243,874 number of mapped reads = 18,078,924 (99.1%) number of supplementary alignments = 66,611 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,073,600 number of mapped paired reads (second in pair) = 9,005,324 number of mapped paired reads (both in pair) = 17,974,752 number of mapped paired reads (singletons) = 104,172 number of mapped bases = 1,785,893,490 bp number of sequenced bases = 1,785,638,962 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,668,839 duplication rate = 47.58% >>>>>>> Insert size mean insert size = 23,605.5544 std insert size = 1,533,822.7739 median insert size = 255 >>>>>>> Mapping quality mean mapping quality = 55.2648 >>>>>>> ACTG content number of A's = 497,208,092 bp (27.84%) number of C's = 398,283,044 bp (22.3%) number of T's = 494,680,584 bp (27.7%) number of G's = 395,124,420 bp (22.13%) number of N's = 342,822 bp (0.02%) GC percentage = 44.43% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 11,343,740 number of insertions = 107,716 mapped reads with insertion percentage = 0.59% number of deletions = 99,516 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.53% >>>>>>> Coverage mean coverageData = 0.5769X std coverageData = 20.0152X There is a 4.8% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 182417605 0.7318641946332403 22.309120011269382 chr2 243199373 145733929 0.5992364503341051 27.50777921964619 chr3 198022430 174097484 0.87918062615432 21.12178113014438 chr4 191154276 57407459 0.30032003573909066 11.862429621363027 chr5 180915260 127964331 0.7073164032707909 23.703916734145036 chr6 171115067 105232776 0.6149825251799714 16.08065833503273 chr7 159138663 64957346 0.4081807951346179 13.139896421588205 chr8 146364022 71254667 0.4868318458753477 14.05710652317486 chr9 141213431 116644676 0.8260168680413975 20.30014774870755 chr10 135534747 54286791 0.40053781190147497 16.11745147843967 chr11 135006516 81896858 0.6066141133513882 25.71540533282121 chr12 133851895 124980737 0.9337240761514807 33.34208919956943 chr13 115169878 29409581 0.2553582717175406 9.470687010977757 chr14 107349540 34134174 0.31797224282470143 9.940248393162491 chr15 102531392 46810048 0.45654357252849936 18.027957827147404 chr16 90354753 56198080 0.6219714861043336 18.179925981716078 chr17 81195210 61497785 0.7574065637615816 15.603051803567169 chr18 78077248 26604061 0.3407402499637282 10.560421504547676 chr19 59128983 33806849 0.5717475133979558 13.92718161692854 chr20 63025520 49367589 0.7832952270762701 32.73997165227791 chr21 48129895 7829181 0.16266773488701772 7.508034040235333 chr22 51304566 16714288 0.3257855840745247 10.334401456245084 chrMT 16571 1947 0.11749441795908515 0.5896865895253263 chrX 155270560 114237818 0.7357339214851805 23.110918441306527 chrY 59373566 2407430 0.04054716875183141 1.7043677831694193