BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472409.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 = 18,376,138 number of mapped reads = 18,205,789 (99.07%) number of supplementary alignments = 112,364 (0.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,127,879 number of mapped paired reads (second in pair) = 9,077,910 number of mapped paired reads (both in pair) = 18,096,556 number of mapped paired reads (singletons) = 109,233 number of mapped bases = 1,781,503,181 bp number of sequenced bases = 1,781,271,792 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,159,190 duplication rate = 45.91% >>>>>>> Insert size mean insert size = 119,390.8962 std insert size = 3,425,788.5941 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 54.8761 >>>>>>> ACTG content number of A's = 492,737,640 bp (27.66%) number of C's = 399,692,253 bp (22.44%) number of T's = 488,610,831 bp (27.43%) number of G's = 400,006,779 bp (22.46%) number of N's = 224,289 bp (0.01%) GC percentage = 44.89% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 9,992,496 number of insertions = 114,764 mapped reads with insertion percentage = 0.62% number of deletions = 97,732 mapped reads with deletion percentage = 0.53% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 0.5755X std coverageData = 16.9409X There is a 5.67% of reference with a coverageData >= 1X There is a 2.34% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% 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 0.29% 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 0.26% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.25% 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 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% 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 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% 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 208753299 0.8375236866511157 20.717172432366226 chr2 243199373 146312850 0.6016168882145926 17.886776838941543 chr3 198022430 150483039 0.7599292615488054 17.176022865032323 chr4 191154276 54278362 0.28395055101984745 8.941114600924976 chr5 180915260 86994083 0.4808554181664941 12.607502179865358 chr6 171115067 112579318 0.6579158689748811 14.795279817859518 chr7 159138663 115277750 0.7243855630482455 24.473847748836175 chr8 146364022 109786989 0.7500954640341873 18.777225235322884 chr9 141213431 78821687 0.5581741512958495 13.278799791716432 chr10 135534747 52945953 0.39064486540857307 15.415454335870763 chr11 135006516 83300717 0.6170125670082472 19.542802146014797 chr12 133851895 82444115 0.6159353590025752 16.8775840089357 chr13 115169878 27234122 0.2364691399603636 7.132226902503077 chr14 107349540 59286837 0.5522784447888645 23.805918898655822 chr15 102531392 44273161 0.4318010331899132 13.42426921516953 chr16 90354753 84783729 0.9383427676461027 24.783276096305084 chr17 81195210 68970156 0.8494362660063322 19.732610157016563 chr18 78077248 48889692 0.6261707892163413 22.480165485067864 chr19 59128983 39163497 0.662340108234231 14.645607419863088 chr20 63025520 28183983 0.4471836646488597 10.558728101251548 chr21 48129895 14839157 0.3083147594649853 13.919942233727358 chr22 51304566 21266722 0.4145190897823792 14.910509401124482 chrMT 16571 2626 0.15846961559350672 0.585662316845198 chrX 155270560 60210245 0.38777631123375866 10.63575756833885 chrY 59373566 2421092 0.04077727115127294 1.6213616629171554