BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046481.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 4,977,180 number of mapped reads = 4,947,865 (99.41%) number of supplementary alignments = 26,862 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,476,451 number of mapped paired reads (second in pair) = 2,471,414 number of mapped paired reads (both in pair) = 4,928,596 number of mapped paired reads (singletons) = 19,269 number of mapped bases = 460,606,748 bp number of sequenced bases = 460,420,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,552,383 duplication rate = 38.41% >>>>>>> Insert size mean insert size = 20,351.0903 std insert size = 1,409,819.7966 median insert size = 110 >>>>>>> Mapping quality mean mapping quality = 51.1109 >>>>>>> ACTG content number of A's = 128,282,416 bp (27.86%) number of C's = 102,597,556 bp (22.28%) number of T's = 125,513,125 bp (27.26%) number of G's = 103,992,055 bp (22.59%) number of N's = 35,509 bp (0.01%) GC percentage = 44.87% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 1,692,538 number of insertions = 45,845 mapped reads with insertion percentage = 0.9% number of deletions = 59,874 mapped reads with deletion percentage = 1.17% homopolymer indels = 47.69% >>>>>>> Coverage mean coverageData = 0.1488X std coverageData = 18.1685X There is a 1.67% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 72082644 0.2891974499834847 24.35813451416773 chr2 243199373 23826778 0.09797220159774014 9.121431278937278 chr3 198022430 20950458 0.10579840879641766 10.24427531588139 chr4 191154276 6524963 0.034134538533681556 1.040680051891779 chr5 180915260 21867994 0.12087423692174999 18.44559412503534 chr6 171115067 44278375 0.2587637417107168 37.43363444596341 chr7 159138663 41359691 0.25989718790084343 26.969739512530396 chr8 146364022 12119630 0.08280470729343581 6.650620092742373 chr9 141213431 5120535 0.036260963024119144 2.0299890873491866 chr10 135534747 28432034 0.20977671504415027 27.556988723550738 chr11 135006516 6026791 0.044640741636499975 1.5543750963564358 chr12 133851895 31764332 0.2373095427599288 22.06220435954763 chr13 115169878 26531249 0.230366216069101 24.616520492921993 chr14 107349540 21442905 0.19974845723605336 13.932454191216516 chr15 102531392 19583742 0.191002400513591 15.600719475077826 chr16 90354753 8429430 0.09329260188448525 6.80972747048734 chr17 81195210 23374230 0.2878769572737111 22.741007463268083 chr18 78077248 8034961 0.10291040227237518 9.143806324419396 chr19 59128983 6180298 0.10452231184155493 5.007695919551181 chr20 63025520 6286886 0.09975143402228177 3.8263399417221393 chr21 48129895 1891583 0.03930162324268524 4.710231577225803 chr22 51304566 15703673 0.30608723987646635 34.704928350895514 chrMT 16571 33023 1.9928187797960293 2.1215851270229087 chrX 155270560 8638758 0.05563680584394105 6.5343689118353945 chrY 59373566 121785 0.002051165328355046 0.2002412002733012