BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472573.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 = 7,606,918 number of mapped reads = 6,972,320 (91.66%) number of supplementary alignments = 210,320 (2.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,513,495 number of mapped paired reads (second in pair) = 3,458,825 number of mapped paired reads (both in pair) = 6,811,314 number of mapped paired reads (singletons) = 161,006 number of mapped bases = 561,133,764 bp number of sequenced bases = 560,897,750 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,067,978 duplication rate = 13.59% >>>>>>> Insert size mean insert size = 231,221.8401 std insert size = 4,649,341.2185 median insert size = 125 >>>>>>> Mapping quality mean mapping quality = 50.3517 >>>>>>> ACTG content number of A's = 143,468,804 bp (25.58%) number of C's = 112,581,677 bp (20.07%) number of T's = 166,490,530 bp (29.68%) number of G's = 137,987,486 bp (24.6%) number of N's = 369,253 bp (0.07%) GC percentage = 44.67% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 6,671,491 number of insertions = 55,279 mapped reads with insertion percentage = 0.78% number of deletions = 125,674 mapped reads with deletion percentage = 1.77% homopolymer indels = 42.55% >>>>>>> Coverage mean coverageData = 0.1813X std coverageData = 1.7404X There is a 10.36% of reference with a coverageData >= 1X There is a 4.54% of reference with a coverageData >= 2X There is a 1.44% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 36527483 0.1465492156186042 2.0467254025752903 chr2 243199373 55963925 0.23011541645709752 2.458509240723626 chr3 198022430 29394338 0.14843943688601335 0.565779956172637 chr4 191154276 27995425 0.146454610306494 0.9727950212025855 chr5 180915260 26484610 0.14639234965585546 0.5926542092047838 chr6 171115067 36970642 0.2160571985165982 1.0003818185624278 chr7 159138663 47375394 0.2976988313644435 3.257846592754363 chr8 146364022 27239889 0.18611055249629585 1.4719395057107583 chr9 141213431 19240820 0.1362534701107857 1.7609271651479297 chr10 135534747 21707930 0.16016505346780188 1.535552249571854 chr11 135006516 20472733 0.1516425547934294 1.296232902360491 chr12 133851895 28693770 0.21436954628098467 0.7085169739297963 chr13 115169878 26107341 0.22668549670600502 0.7317721312614166 chr14 107349540 14558173 0.13561467520028497 4.179295926766448 chr15 102531392 13251295 0.129241344933657 0.5341198002140144 chr16 90354753 21057297 0.23305134816759446 1.070790297233869 chr17 81195210 22447118 0.2764586482379934 1.4772507501244985 chr18 78077248 12260840 0.15703473565051884 2.941855131641465 chr19 59128983 12902744 0.21821352821170625 1.486832506654784 chr20 63025520 19961423 0.3167196875170566 1.0933765641578916 chr21 48129895 8555841 0.17776562778705418 0.8066890195143743 chr22 51304566 5805897 0.11316530774278453 0.5085324474049133 chrMT 16571 63852 3.8532375837306136 3.7675609188131323 chrX 155270560 24759643 0.15946128486945627 0.8238497941012651 chrY 59373566 1335341 0.022490496865221133 0.7952069115402335