BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068159.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,530,643 number of mapped reads = 4,333,770 (95.65%) number of supplementary alignments = 33,916 (0.75%) number of secondary alignments = 0 number of mapped bases = 283,941,351 bp number of sequenced bases = 283,821,860 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 461,613 duplication rate = 8.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1651 >>>>>>> ACTG content number of A's = 77,140,915 bp (27.18%) number of C's = 51,049,596 bp (17.99%) number of T's = 92,232,960 bp (32.5%) number of G's = 63,365,269 bp (22.33%) number of N's = 33,120 bp (0.01%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,579,941 number of insertions = 18,135 mapped reads with insertion percentage = 0.42% number of deletions = 68,156 mapped reads with deletion percentage = 1.56% homopolymer indels = 44.92% >>>>>>> Coverage mean coverageData = 0.0917X std coverageData = 0.8735X There is a 6.78% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% 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 32509691 0.13042972920015314 1.9304965713468905 chr2 243199373 30121854 0.12385662688365566 0.9403171920907729 chr3 198022430 21026100 0.10618039582687679 0.4209153371278115 chr4 191154276 15195274 0.0794922003209596 0.38029301436147495 chr5 180915260 12240853 0.0676606992688179 0.33913606870928126 chr6 171115067 19172647 0.11204534665553444 0.5357092482205643 chr7 159138663 31585710 0.19847917158886774 1.6037180958648936 chr8 146364022 11785462 0.08052157790525871 0.9470439617059229 chr9 141213431 8095533 0.057328350020756876 0.6709313798148053 chr10 135534747 12261032 0.09046412282748423 0.6784299673288386 chr11 135006516 15611429 0.11563463351650376 0.6289163525075467 chr12 133851895 6865482 0.05129163094777254 0.338334818995731 chr13 115169878 7034944 0.06108319399279037 0.3247883472418715 chr14 107349540 4898634 0.045632556972298156 0.365210408429075 chr15 102531392 4622251 0.045081324946802635 0.30145494673471157 chr16 90354753 6350338 0.07028227945020225 0.4097594438453745 chr17 81195210 7036878 0.08666617156356883 0.41234535377868076 chr18 78077248 6119160 0.07837315167665745 1.318689818359907 chr19 59128983 5220477 0.08828964638204584 1.1737876047158782 chr20 63025520 4443989 0.07051094540751111 0.37723291821329713 chr21 48129895 6428973 0.13357546281785987 0.4949608754312103 chr22 51304566 3111011 0.06063809213394379 0.30886630618648414 chrMT 16571 242493 14.633576730432683 8.64587353810674 chrX 155270560 11319235 0.07290007197758545 0.4245592009661586 chrY 59373566 641901 0.010811225318688118 0.30716386743211466