BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084839.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 = 2,048,912 number of mapped reads = 1,870,603 (91.3%) number of supplementary alignments = 23,963 (1.17%) number of secondary alignments = 0 number of mapped bases = 125,598,843 bp number of sequenced bases = 125,551,753 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,235 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8838 >>>>>>> ACTG content number of A's = 34,694,777 bp (27.63%) number of C's = 23,322,269 bp (18.58%) number of T's = 39,780,386 bp (31.68%) number of G's = 27,736,785 bp (22.09%) number of N's = 17,536 bp (0.01%) GC percentage = 40.67% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 928,707 number of insertions = 9,658 mapped reads with insertion percentage = 0.51% number of deletions = 29,155 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.51% >>>>>>> Coverage mean coverageData = 0.0406X std coverageData = 0.3076X There is a 3.44% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 14204456 0.056988648385353474 0.5179918747087142 chr2 243199373 10305285 0.0423738140147261 0.4397481277551141 chr3 198022430 9668982 0.04882771108303236 0.2547961965817309 chr4 191154276 5711780 0.029880472043429467 0.20212527286278933 chr5 180915260 5681470 0.03140403965923051 0.20187326719400472 chr6 171115067 8708062 0.05089009490905906 0.2959360562489431 chr7 159138663 9574271 0.06016307300508111 0.3989444890054454 chr8 146364022 8610558 0.05882974437529463 0.3702644458839285 chr9 141213431 4869246 0.034481465151852304 0.24644577535859225 chr10 135534747 5832202 0.043031046496143165 0.27226207986887246 chr11 135006516 4486596 0.03323244042531991 0.2333558959350741 chr12 133851895 4350583 0.03250296157555334 0.20698032358323767 chr13 115169878 4137799 0.035927788340628444 0.21703726127359882 chr14 107349540 2925451 0.0272516398300356 0.18915539403922577 chr15 102531392 2901536 0.028299001343900607 0.2011494960620834 chr16 90354753 3582107 0.03964492050573145 0.23414939049092018 chr17 81195210 2628247 0.03236948337223341 0.20985756269103578 chr18 78077248 2860479 0.036636524381597056 0.3832008890200004 chr19 59128983 3181663 0.05380885715555094 0.38333962802399757 chr20 63025520 2758823 0.04377310968636197 0.24072748669038352 chr21 48129895 1934512 0.04019356368843107 0.23159787513763153 chr22 51304566 1081976 0.021089273028837237 0.16350442190116965 chrMT 16571 112154 6.768088829883531 4.381372167221302 chrX 155270560 5256162 0.03385163291740559 0.21511102048922473 chrY 59373566 234443 0.003948609049353714 0.08171514981397794