BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083676.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 = 2,314,846 number of mapped reads = 1,843,180 (79.62%) number of supplementary alignments = 12,816 (0.55%) number of secondary alignments = 0 number of mapped bases = 109,532,143 bp number of sequenced bases = 109,498,422 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,984 duplication rate = 2.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.266 >>>>>>> ACTG content number of A's = 32,558,354 bp (29.73%) number of C's = 21,218,668 bp (19.38%) number of T's = 32,043,250 bp (29.26%) number of G's = 23,663,198 bp (21.61%) number of N's = 14,952 bp (0.01%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 919,520 number of insertions = 7,380 mapped reads with insertion percentage = 0.4% number of deletions = 21,412 mapped reads with deletion percentage = 1.15% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 0.0354X std coverageData = 0.2875X There is a 3.16% of reference with a coverageData >= 1X There is a 0.3% 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 11353371 0.045550020916497534 0.5820020643489281 chr2 243199373 9626570 0.03958303790528276 0.2579579221850626 chr3 198022430 8629807 0.04357994697873367 0.22976791583946718 chr4 191154276 5653530 0.02957574435844689 0.19204881225616516 chr5 180915260 5597645 0.030940701187948436 0.19286143517026835 chr6 171115067 7617545 0.0445170909467604 0.2603606233927208 chr7 159138663 7492778 0.04708332883254147 0.37087556625716994 chr8 146364022 7617773 0.0520467591413961 0.3917431064174221 chr9 141213431 4101385 0.0290438733125888 0.21384105697724243 chr10 135534747 4603654 0.03396659603459473 0.24961405252349167 chr11 135006516 3976528 0.029454341300089545 0.21626360191836896 chr12 133851895 3975409 0.02970005766448058 0.18808808296952512 chr13 115169878 3305996 0.02870538770562907 0.18391749059247553 chr14 107349540 2562760 0.02387304128177913 0.16961424793121746 chr15 102531392 2509623 0.024476630532822573 0.17161657778464756 chr16 90354753 2917397 0.03228825162080848 0.2026811474960064 chr17 81195210 2340626 0.028827143867230592 0.19182656987517482 chr18 78077248 3047062 0.039026247441508184 0.3584056092842153 chr19 59128983 2769041 0.04683051964550109 0.4027813025387202 chr20 63025520 2168098 0.03440031910883084 0.20721409689263023 chr21 48129895 1852696 0.03849366386525464 0.2166785551639971 chr22 51304566 804765 0.01568603075211668 0.13434595299805915 chrMT 16571 5316 0.32080140003620783 0.6199380619190815 chrX 155270560 4765013 0.030688451178381787 0.19963770203823597 chrY 59373566 237755 0.004004391449218327 0.093247527619343