BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472434.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 = 20,486,528 number of mapped reads = 20,268,262 (98.93%) number of supplementary alignments = 72,086 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,165,838 number of mapped paired reads (second in pair) = 10,102,424 number of mapped paired reads (both in pair) = 20,168,360 number of mapped paired reads (singletons) = 99,902 number of mapped bases = 1,981,627,924 bp number of sequenced bases = 1,981,417,808 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,159,374 duplication rate = 48.86% >>>>>>> Insert size mean insert size = 15,569.3283 std insert size = 1,247,345.1779 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 54.7474 >>>>>>> ACTG content number of A's = 534,099,832 bp (26.96%) number of C's = 458,584,360 bp (23.14%) number of T's = 535,102,021 bp (27.01%) number of G's = 453,384,818 bp (22.88%) number of N's = 246,777 bp (0.01%) GC percentage = 46.03% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 10,206,866 number of insertions = 115,992 mapped reads with insertion percentage = 0.57% number of deletions = 85,233 mapped reads with deletion percentage = 0.41% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 0.6401X std coverageData = 19.7937X There is a 5.39% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% 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 0.31% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.27% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 166559964 0.6682429248591522 19.72141743175551 chr2 243199373 144102334 0.5925275720180413 18.122582490592013 chr3 198022430 141838200 0.7162734039775192 16.470363662480317 chr4 191154276 47411656 0.24802822616429465 8.391530182206663 chr5 180915260 73438730 0.4059288862642101 13.902157513020835 chr6 171115067 155698437 0.909904894581843 21.541497080959495 chr7 159138663 132797522 0.8344767983880824 27.07215615831928 chr8 146364022 157884276 1.0787096025551963 28.101578355054844 chr9 141213431 75841946 0.5370731768425059 16.176558298870116 chr10 135534747 37217275 0.2745958200667169 12.230378176974067 chr11 135006516 58029937 0.4298306386930243 11.60674714328165 chr12 133851895 95056954 0.7101651717370158 16.755349051497397 chr13 115169878 63719449 0.5532648823332087 16.36688790400111 chr14 107349540 37396076 0.34835804606149223 11.799534803539524 chr15 102531392 40856462 0.3984775901608748 13.1727701641788 chr16 90354753 123622081 1.3681857002032864 36.231088473624844 chr17 81195210 70136555 0.863801633125895 17.888030418289 chr18 78077248 15957921 0.20438631494798587 8.798344755271968 chr19 59128983 43494020 0.7355786924324405 16.035325785509325 chr20 63025520 122175493 1.9385082899752355 47.783524779149744 chr21 48129895 13273778 0.2757907117811082 12.844334007466296 chr22 51304566 32796036 0.6392420510876167 23.69186898457107 chrMT 16571 1026 0.06191539436364733 0.24497543290917675 chrX 155270560 131932661 0.849695273849724 25.233469784337384 chrY 59373566 389135 0.006554010921291135 0.5304146339683422