BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618638.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 71,709,530 number of mapped reads = 65,892,090 (91.89%) number of supplementary alignments = 380,637 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 34,531,072 number of mapped paired reads (second in pair) = 31,361,018 number of mapped paired reads (both in pair) = 62,004,262 number of mapped paired reads (singletons) = 3,887,828 number of mapped bases = 6,102,311,175 bp number of sequenced bases = 6,098,004,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,341,977 duplication rate = 24.13% >>>>>>> Insert size mean insert size = 133,169.4133 std insert size = 3,650,695.0686 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 52.5261 >>>>>>> ACTG content number of A's = 1,660,375,787 bp (27.23%) number of C's = 1,325,169,109 bp (21.73%) number of T's = 1,686,683,402 bp (27.66%) number of G's = 1,424,667,366 bp (23.36%) number of N's = 1,108,879 bp (0.02%) GC percentage = 45.09% >>>>>>> Mismatches and indels general error rate = 0.0148 number of mismatches = 88,584,686 number of insertions = 1,133,129 mapped reads with insertion percentage = 1.69% number of deletions = 3,110,083 mapped reads with deletion percentage = 4.6% homopolymer indels = 52.44% >>>>>>> Coverage mean coverageData = 1.9712X std coverageData = 7.7925X There is a 31.94% of reference with a coverageData >= 1X There is a 22.62% of reference with a coverageData >= 2X There is a 17.46% of reference with a coverageData >= 3X There is a 14.09% of reference with a coverageData >= 4X There is a 11.66% of reference with a coverageData >= 5X There is a 9.84% of reference with a coverageData >= 6X There is a 8.41% of reference with a coverageData >= 7X There is a 7.27% of reference with a coverageData >= 8X There is a 6.35% of reference with a coverageData >= 9X There is a 5.58% of reference with a coverageData >= 10X There is a 4.94% of reference with a coverageData >= 11X There is a 4.39% of reference with a coverageData >= 12X There is a 3.93% of reference with a coverageData >= 13X There is a 3.53% of reference with a coverageData >= 14X There is a 3.18% of reference with a coverageData >= 15X There is a 2.88% of reference with a coverageData >= 16X There is a 2.61% of reference with a coverageData >= 17X There is a 2.37% of reference with a coverageData >= 18X There is a 2.17% of reference with a coverageData >= 19X There is a 1.98% of reference with a coverageData >= 20X There is a 1.82% of reference with a coverageData >= 21X There is a 1.67% of reference with a coverageData >= 22X There is a 1.53% of reference with a coverageData >= 23X There is a 1.42% of reference with a coverageData >= 24X There is a 1.31% of reference with a coverageData >= 25X There is a 1.21% of reference with a coverageData >= 26X There is a 1.12% of reference with a coverageData >= 27X There is a 1.04% of reference with a coverageData >= 28X There is a 0.97% of reference with a coverageData >= 29X There is a 0.9% of reference with a coverageData >= 30X There is a 0.84% of reference with a coverageData >= 31X There is a 0.78% of reference with a coverageData >= 32X There is a 0.73% of reference with a coverageData >= 33X There is a 0.68% of reference with a coverageData >= 34X There is a 0.64% of reference with a coverageData >= 35X There is a 0.6% of reference with a coverageData >= 36X There is a 0.56% of reference with a coverageData >= 37X There is a 0.52% of reference with a coverageData >= 38X There is a 0.49% of reference with a coverageData >= 39X There is a 0.46% of reference with a coverageData >= 40X There is a 0.43% of reference with a coverageData >= 41X There is a 0.41% of reference with a coverageData >= 42X There is a 0.38% of reference with a coverageData >= 43X There is a 0.36% of reference with a coverageData >= 44X There is a 0.34% of reference with a coverageData >= 45X There is a 0.32% of reference with a coverageData >= 46X There is a 0.3% of reference with a coverageData >= 47X There is a 0.29% of reference with a coverageData >= 48X There is a 0.27% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 553541296 2.220822133879458 8.65786155348504 chr2 243199373 530571782 2.181633017614729 10.3074405125315 chr3 198022430 416839206 2.105010053659073 6.185012005916353 chr4 191154276 332275840 1.7382600428985433 6.152364381682534 chr5 180915260 352754858 1.9498347347813556 6.003940621484348 chr6 171115067 341473706 1.9955794190817808 6.149244979712211 chr7 159138663 318822814 2.0034277528145377 6.342638461671033 chr8 146364022 303331226 2.0724439097471645 6.424227326573158 chr9 141213431 278091295 1.9692977716829216 8.300173547177668 chr10 135534747 328261523 2.4219731859609404 7.163482843577936 chr11 135006516 315718344 2.3385415263956593 7.711303914230964 chr12 133851895 285198933 2.1307052320775886 6.698825902400794 chr13 115169878 172111721 1.4944161093927701 5.1357875411057785 chr14 107349540 205866095 1.9177175328371225 6.573684153247059 chr15 102531392 205364631 2.002943947157179 6.985146679720419 chr16 90354753 217620973 2.4085171590253807 18.09804186565449 chr17 81195210 200457318 2.468831819019866 7.75003632838869 chr18 78077248 162636101 2.0830152850674244 8.002507532601907 chr19 59128983 133700526 2.261167353411101 8.113376932473923 chr20 63025520 173807653 2.7577345335667203 8.083360752464547 chr21 48129895 86605051 1.7994024503897215 9.379848960774785 chr22 51304566 106332103 2.072566075307995 7.338255788077279 chrMT 16571 41218 2.487357431657715 9.215127063533027 chrX 155270560 22750125 0.1465192435707065 2.3449066317471243 chrY 59373566 58136837 0.979170376931714 7.901198560724714