BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080616.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 = 6,076,218 number of mapped reads = 5,139,313 (84.58%) number of supplementary alignments = 38,239 (0.63%) number of secondary alignments = 0 number of mapped bases = 340,572,477 bp number of sequenced bases = 340,437,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 286,373 duplication rate = 4.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1849 >>>>>>> ACTG content number of A's = 93,815,050 bp (27.56%) number of C's = 59,724,993 bp (17.54%) number of T's = 111,726,419 bp (32.82%) number of G's = 74,894,013 bp (22%) number of N's = 277,162 bp (0.08%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,009,322 number of insertions = 27,801 mapped reads with insertion percentage = 0.54% number of deletions = 82,942 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.6% >>>>>>> Coverage mean coverageData = 0.11X std coverageData = 0.6869X There is a 8.57% of reference with a coverageData >= 1X There is a 1.69% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.11% 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 0.01% 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 35226246 0.1413286187960992 0.9941116410034749 chr2 243199373 24900924 0.10238893173462252 0.7103489068708568 chr3 198022430 23096626 0.1166364133598401 0.4127653422641924 chr4 191154276 18171118 0.09505996088729922 0.3908567841289819 chr5 180915260 19036505 0.10522332389208075 0.38964525355373575 chr6 171115067 20404808 0.11924612109113687 0.6491794440766406 chr7 159138663 20386222 0.12810351435464806 1.4462130776114879 chr8 146364022 31606508 0.21594451674742854 1.1042648169883875 chr9 141213431 12115396 0.08579492697121706 0.5793583775365602 chr10 135534747 15772488 0.11637228348535597 0.656353783156407 chr11 135006516 14894531 0.1103245342617389 0.5306089252298277 chr12 133851895 12163753 0.09087471641697714 0.3757901417799056 chr13 115169878 8905656 0.07732626060435699 0.33154513024690296 chr14 107349540 8094215 0.07540055597816255 0.3706217635091416 chr15 102531392 7422331 0.07239081470775312 0.3274832182457311 chr16 90354753 8669855 0.09595350230219765 0.4198873290981818 chr17 81195210 6453915 0.07948640073718634 0.38898728820808676 chr18 78077248 11381928 0.14577778151197132 0.9738609768484553 chr19 59128983 4895762 0.08279800787373597 0.7373018996272412 chr20 63025520 7467134 0.11847794353779231 0.43767983811243155 chr21 48129895 4137455 0.08596434710692803 0.39214218641672427 chr22 51304566 3193670 0.06224923528248928 0.29740470781995637 chrMT 16571 245558 14.818538410476133 20.5584768037326 chrX 155270560 21210355 0.1366025536328329 0.515426654401563 chrY 59373566 719518 0.012118490575418698 0.2177871245458888