BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081953.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,668,611 number of mapped reads = 2,441,294 (91.48%) number of supplementary alignments = 17,782 (0.67%) number of secondary alignments = 0 number of mapped bases = 165,619,401 bp number of sequenced bases = 165,553,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,999 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.572 >>>>>>> ACTG content number of A's = 46,047,795 bp (27.81%) number of C's = 31,042,667 bp (18.75%) number of T's = 51,555,419 bp (31.14%) number of G's = 36,886,960 bp (22.28%) number of N's = 21,021 bp (0.01%) GC percentage = 41.03% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,262,838 number of insertions = 11,919 mapped reads with insertion percentage = 0.48% number of deletions = 36,451 mapped reads with deletion percentage = 1.48% homopolymer indels = 48.25% >>>>>>> Coverage mean coverageData = 0.0535X std coverageData = 0.4097X There is a 4.47% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 15149070 0.06077846441955304 0.604268305872571 chr2 243199373 14368216 0.059079987841909445 0.5749714948822038 chr3 198022430 10223969 0.051630358237700645 0.2624268576337137 chr4 191154276 8989373 0.047026795257250745 0.263923441953792 chr5 180915260 8329801 0.04604255605635478 0.24794258975988986 chr6 171115067 13977077 0.08168232783381957 0.3833056046349562 chr7 159138663 11304114 0.07103310903146146 0.5139069581966224 chr8 146364022 9370636 0.06402281019580071 0.64917172817875 chr9 141213431 8135889 0.057614130202671726 0.44627690255988284 chr10 135534747 6520635 0.048110430309063104 0.40042295826359015 chr11 135006516 7342554 0.054386663825914894 0.3299120048724442 chr12 133851895 6980002 0.05214720344452352 0.2686934995566386 chr13 115169878 4431159 0.0384749821476758 0.22557563668212516 chr14 107349540 4263954 0.039720281987235345 0.24900686864509888 chr15 102531392 3820576 0.03726250005461742 0.22872194176601443 chr16 90354753 3751002 0.041514163621254103 0.2643996908365208 chr17 81195210 4822922 0.059399095094402735 0.29741417184878055 chr18 78077248 4325808 0.055404206869586387 0.6558638138635317 chr19 59128983 3848919 0.06509361069173134 0.522200259233358 chr20 63025520 3959819 0.06282881918308647 0.2952804550605791 chr21 48129895 1819935 0.03781298504806628 0.2499196626981663 chr22 51304566 1473325 0.02871722957367966 0.19429967040482712 chrMT 16571 101287 6.11230462856798 3.8440797147084225 chrX 155270560 7941798 0.05114812492464766 0.28936146624299636 chrY 59373566 367561 0.006190650566617474 0.13420522026803294