BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234094.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,136,279 number of mapped reads = 1,943,100 (90.96%) number of supplementary alignments = 14,678 (0.69%) number of secondary alignments = 0 number of mapped bases = 133,984,216 bp number of sequenced bases = 133,925,056 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,463 duplication rate = 4.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9171 >>>>>>> ACTG content number of A's = 38,608,748 bp (28.83%) number of C's = 24,944,015 bp (18.63%) number of T's = 41,990,934 bp (31.35%) number of G's = 28,368,722 bp (21.18%) number of N's = 12,637 bp (0.01%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 989,187 number of insertions = 10,559 mapped reads with insertion percentage = 0.54% number of deletions = 33,419 mapped reads with deletion percentage = 1.7% homopolymer indels = 44.79% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.7071X There is a 3.75% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 12999277 0.05215343876715958 1.6919931724141377 chr2 243199373 6622865 0.027232245372606285 0.573226828654675 chr3 198022430 14486875 0.07315774783694959 0.2990811394970839 chr4 191154276 5210550 0.027258349167140785 0.19767559269558094 chr5 180915260 9028455 0.04990433090055532 0.2581576804062424 chr6 171115067 9064663 0.05297407854797497 0.3523484826874913 chr7 159138663 9652868 0.06065696304109329 1.0219475234943456 chr8 146364022 5127443 0.03503212695261954 1.164095326179045 chr9 141213431 4856551 0.03439156577110573 0.4606758706414511 chr10 135534747 6538157 0.04823971081009949 0.5146662966707612 chr11 135006516 6037339 0.04471887119877977 0.4474389345869309 chr12 133851895 4893573 0.03655960941008717 0.22726674498263003 chr13 115169878 7976046 0.06925461881621513 0.2906779053115516 chr14 107349540 7021645 0.06540917641566046 0.34276916239590105 chr15 102531392 2888307 0.02816997744456644 0.19184321080384498 chr16 90354753 1821653 0.020161119802961557 0.317297945555013 chr17 81195210 3075882 0.03788255489455597 0.2717800958966632 chr18 78077248 2934542 0.037585110581766404 1.2614855231394573 chr19 59128983 3151891 0.05330534773446044 0.8431826648506746 chr20 63025520 2332838 0.03701418092226768 0.2744525788642126 chr21 48129895 2431537 0.05052030551905422 0.26759151515809 chr22 51304566 809346 0.015775321050372007 0.13583202623281693 chrMT 16571 77390 4.670206988111762 3.4013015199762706 chrX 155270560 4642288 0.029898056656715865 0.2866221579990807 chrY 59373566 302235 0.005090396625326496 0.11231632666333287