BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080662.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 = 1,384,530 number of mapped reads = 1,256,253 (90.73%) number of supplementary alignments = 9,544 (0.69%) number of secondary alignments = 0 number of mapped bases = 82,961,412 bp number of sequenced bases = 82,933,642 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,581 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5391 >>>>>>> ACTG content number of A's = 21,419,940 bp (25.83%) number of C's = 16,221,374 bp (19.56%) number of T's = 25,311,195 bp (30.52%) number of G's = 19,977,607 bp (24.09%) number of N's = 3,526 bp (0%) GC percentage = 43.65% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 573,053 number of insertions = 5,715 mapped reads with insertion percentage = 0.45% number of deletions = 17,262 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 0.0268X std coverageData = 0.2274X There is a 2.35% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 10255414 0.041144988762134314 0.26762433862727064 chr2 243199373 5345403 0.02197950979092368 0.31424860437550073 chr3 198022430 5274648 0.026636618892112374 0.18052223552325078 chr4 191154276 3457874 0.01808944101255679 0.1505631866738628 chr5 180915260 3657393 0.020216055848467397 0.15664580136344655 chr6 171115067 4844465 0.028311153920770753 0.22145736435260183 chr7 159138663 5139753 0.032297324252372285 0.44876490644937356 chr8 146364022 9664320 0.06602934155498952 0.3075403075393206 chr9 141213431 2629508 0.018620806685165803 0.16934436265432534 chr10 135534747 4088340 0.0301645156721324 0.1983434372082649 chr11 135006516 3578625 0.026507053926197163 0.19038971485059938 chr12 133851895 2703721 0.020199347943486344 0.15853450229831298 chr13 115169878 1610119 0.013980382960898857 0.13071729365117568 chr14 107349540 1583101 0.014747161468973225 0.1373113653490896 chr15 102531392 1523151 0.014855460072169898 0.14237121819733625 chr16 90354753 2271106 0.025135434767886534 0.18124254917063834 chr17 81195210 1513467 0.01863985572547937 0.1534322331015517 chr18 78077248 2489235 0.03188169490809922 0.24652584663735536 chr19 59128983 1603332 0.027115839283080517 0.20352603391405436 chr20 63025520 2209837 0.035062574652299575 0.2118020379355819 chr21 48129895 1252617 0.026025758003419705 0.1832480617183363 chr22 51304566 889531 0.017338242370084564 0.14674380500732775 chrMT 16571 14344 0.8656085933256895 1.1295780422162172 chrX 155270560 5203084 0.03350979090949373 0.20798175977072308 chrY 59373566 159024 0.0026783636340791794 0.06020563790484276