BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472777.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 = 18,660,872 number of mapped reads = 18,379,041 (98.49%) number of supplementary alignments = 64,735 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,248,372 number of mapped paired reads (second in pair) = 9,130,669 number of mapped paired reads (both in pair) = 18,211,076 number of mapped paired reads (singletons) = 167,965 number of mapped bases = 1,808,273,548 bp number of sequenced bases = 1,808,023,622 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,631,137 duplication rate = 47.5% >>>>>>> Insert size mean insert size = 25,373.1936 std insert size = 1,556,267.7627 median insert size = 263 >>>>>>> Mapping quality mean mapping quality = 55.2418 >>>>>>> ACTG content number of A's = 508,348,374 bp (28.12%) number of C's = 398,672,868 bp (22.05%) number of T's = 505,298,349 bp (27.95%) number of G's = 395,359,711 bp (21.87%) number of N's = 344,320 bp (0.02%) GC percentage = 43.92% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 12,462,198 number of insertions = 109,635 mapped reads with insertion percentage = 0.59% number of deletions = 104,435 mapped reads with deletion percentage = 0.56% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.5841X std coverageData = 20.132X There is a 5.38% of reference with a coverageData >= 1X There is a 2.33% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 214364162 0.8600346155205768 37.22134880962007 chr2 243199373 132224763 0.5436887495593996 25.130885076373055 chr3 198022430 211165817 1.0663732234777645 24.674759616534544 chr4 191154276 84919819 0.44424755112462144 17.574911054157795 chr5 180915260 128657599 0.7111484072708958 22.115451736140805 chr6 171115067 113322959 0.6622617223999334 16.463903518384214 chr7 159138663 66869142 0.420194192532584 10.71509050254714 chr8 146364022 79977088 0.546425869603392 14.953227606423235 chr9 141213431 98566018 0.6979932241714317 19.181707167695468 chr10 135534747 42958002 0.31695194738512333 12.559431350395919 chr11 135006516 80938144 0.5995128709195043 19.159268789812785 chr12 133851895 97153067 0.7258251143922916 25.097316230705097 chr13 115169878 46714302 0.40561215146898044 15.241279616615133 chr14 107349540 45037732 0.4195428503932108 14.402445020153474 chr15 102531392 40779223 0.3977242696558728 11.78598757179965 chr16 90354753 54625589 0.604567963347761 13.636351628124652 chr17 81195210 56299261 0.6933815553897822 15.402594620933318 chr18 78077248 31375185 0.4018479877774381 12.769117243855604 chr19 59128983 35952407 0.6080335763596678 15.3935542046256 chr20 63025520 31953330 0.5069903429594869 14.72222044049317 chr21 48129895 8812560 0.1830995060346589 7.012652780066248 chr22 51304566 11773185 0.22947635888782297 6.673180244778857 chrMT 16571 6685 0.40341560557600625 1.1250400907902105 chrX 155270560 91689758 0.5905160514652616 15.748198136443238 chrY 59373566 2137751 0.03600509694836251 1.0009384238290837