BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818990.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,408,771 number of mapped reads = 2,373,019 (98.52%) number of supplementary alignments = 32,978 (1.37%) number of secondary alignments = 0 number of mapped bases = 219,726,227 bp number of sequenced bases = 219,596,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,032,747 duplication rate = 36.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2099 >>>>>>> ACTG content number of A's = 63,632,953 bp (28.98%) number of C's = 47,704,233 bp (21.72%) number of T's = 61,449,175 bp (27.98%) number of G's = 46,798,495 bp (21.31%) number of N's = 11,464 bp (0.01%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,376,371 number of insertions = 33,388 mapped reads with insertion percentage = 1.37% number of deletions = 69,360 mapped reads with deletion percentage = 2.86% homopolymer indels = 41.77% >>>>>>> Coverage mean coverageData = 0.071X std coverageData = 0.8166X There is a 3.34% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% 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% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% 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 22380493 0.08979112232582963 1.4786323529553878 chr2 243199373 17518718 0.07203438801628818 1.0956509259570846 chr3 198022430 11691482 0.05904120053470711 0.4393962498275517 chr4 191154276 11895968 0.06223228822775589 0.5326059278927514 chr5 180915260 11569481 0.06394972430739121 0.4820829752707021 chr6 171115067 9196081 0.05374208806521988 0.535555747228384 chr7 159138663 10868297 0.06829450992685543 1.0544211078426358 chr8 146364022 19974568 0.1364718441530665 0.7661615815632354 chr9 141213431 9404117 0.06659506063555669 0.7937734598319418 chr10 135534747 11682040 0.0861922146060449 0.9929398563035601 chr11 135006516 8211711 0.06082455309045972 0.576901337716803 chr12 133851895 10076479 0.07528080943493554 0.5183908529082334 chr13 115169878 4551709 0.03952169681034133 0.3605333959169592 chr14 107349540 5039835 0.046947895631411184 0.42181741638497233 chr15 102531392 5744979 0.05603141523719877 0.4330262789620174 chr16 90354753 7166102 0.07931073642578604 0.9271195638531029 chr17 81195210 7824000 0.09636036411507526 0.6653172177496638 chr18 78077248 5074357 0.06499149406495475 0.9135335849220503 chr19 59128983 4702303 0.07952619445526402 1.2713874002016643 chr20 63025520 6389007 0.10137174592133472 0.6266195602065964 chr21 48129895 3022784 0.06280470796788566 0.5159957578443697 chr22 51304566 1776864 0.034633642549476006 0.3832778705706721 chrMT 16571 25009 1.509202824210971 2.2454459588271174 chrX 155270560 13107148 0.08441489487768963 0.6208859641777463 chrY 59373566 832695 0.014024675560164266 0.8543698883008085