BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084361.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 = 2,486,386 number of mapped reads = 2,230,069 (89.69%) number of supplementary alignments = 12,640 (0.51%) number of secondary alignments = 0 number of mapped bases = 148,988,697 bp number of sequenced bases = 148,938,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,777 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3623 >>>>>>> ACTG content number of A's = 41,198,491 bp (27.66%) number of C's = 28,836,631 bp (19.36%) number of T's = 45,422,066 bp (30.5%) number of G's = 33,289,388 bp (22.35%) number of N's = 191,526 bp (0.13%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,498,712 number of insertions = 10,546 mapped reads with insertion percentage = 0.47% number of deletions = 28,910 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 0.0481X std coverageData = 0.3415X There is a 4.11% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 14951533 0.059985940817375134 0.5669422228862888 chr2 243199373 14340101 0.0589643831030765 0.38254641922968574 chr3 198022430 10015616 0.050578189551557365 0.2587687641982249 chr4 191154276 7141628 0.037360545363892356 0.23021908746024516 chr5 180915260 7566881 0.04182555412959636 0.23073225707237754 chr6 171115067 7171663 0.04191134729240412 0.25751048259782383 chr7 159138663 8394861 0.05275186332311966 0.514918012057303 chr8 146364022 7518303 0.05136715223636038 0.3165956007757908 chr9 141213431 5507144 0.03899872668627392 0.280904947220902 chr10 135534747 10856554 0.0801016288465127 0.4819543502667412 chr11 135006516 8347846 0.06183291182775208 0.35185064365954327 chr12 133851895 5544197 0.04142038482159704 0.2314177611209998 chr13 115169878 3612378 0.031365649271591654 0.19985027102878444 chr14 107349540 3996536 0.03722918607755562 0.22582264478293432 chr15 102531392 3325488 0.03243385206357093 0.21134065713944408 chr16 90354753 3367078 0.03726508997263265 0.2373146377120005 chr17 81195210 4216319 0.051928174088102 0.2757053326835391 chr18 78077248 4027793 0.051587281867311714 0.4612968387304702 chr19 59128983 3266706 0.05524711967395076 0.41628564710704175 chr20 63025520 3121749 0.049531507237068416 0.25462360095676245 chr21 48129895 1561057 0.032434249025475745 0.2177119126890137 chr22 51304566 1339640 0.026111516078315525 0.18054500560296532 chrMT 16571 43611 2.6317663387846237 2.4221180724630256 chrX 155270560 9419555 0.06066542814040215 0.31231262445657076 chrY 59373566 334460 0.005633146575700035 0.11978560659855986