BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779374.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 17,495,956 number of mapped reads = 15,223,210 (87.01%) number of supplementary alignments = 206,214 (1.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,659,589 number of mapped paired reads (second in pair) = 7,563,621 number of mapped paired reads (both in pair) = 15,069,196 number of mapped paired reads (singletons) = 154,014 number of mapped bases = 1,201,136,049 bp number of sequenced bases = 1,200,838,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,661,011 duplication rate = 18.63% >>>>>>> Insert size mean insert size = 54,785.3321 std insert size = 2,194,400.9084 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 51.415 >>>>>>> ACTG content number of A's = 370,318,783 bp (30.84%) number of C's = 229,613,272 bp (19.12%) number of T's = 367,567,098 bp (30.61%) number of G's = 233,079,541 bp (19.41%) number of N's = 260,287 bp (0.02%) GC percentage = 38.53% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 4,305,440 number of insertions = 141,080 mapped reads with insertion percentage = 0.92% number of deletions = 147,429 mapped reads with deletion percentage = 0.96% homopolymer indels = 48.73% >>>>>>> Coverage mean coverageData = 0.388X std coverageData = 39.1739X There is a 4.44% of reference with a coverageData >= 1X There is a 2.68% of reference with a coverageData >= 2X There is a 1.84% of reference with a coverageData >= 3X There is a 1.44% of reference with a coverageData >= 4X There is a 1.18% of reference with a coverageData >= 5X There is a 1% of reference with a coverageData >= 6X There is a 0.86% of reference with a coverageData >= 7X There is a 0.76% of reference with a coverageData >= 8X There is a 0.68% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.55% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.46% of reference with a coverageData >= 13X There is a 0.43% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.37% of reference with a coverageData >= 16X There is a 0.35% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.31% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 73478571 0.29479794555857897 15.11861435093612 chr2 243199373 106381858 0.4374265307008008 47.08619156238181 chr3 198022430 92098837 0.4650929543688561 29.395576775978604 chr4 191154276 83200850 0.4352549769799552 41.66678826852787 chr5 180915260 116254904 0.6425931344873838 43.86972409638252 chr6 171115067 55155306 0.3223287520321048 6.930808225290381 chr7 159138663 148346994 0.932187007251657 43.27249262072325 chr8 146364022 50334239 0.343897621233721 10.645648836885657 chr9 141213431 49281747 0.34898767525873653 5.897482721506008 chr10 135534747 18863568 0.139178833601984 4.939868322774903 chr11 135006516 121463483 0.8996860788556309 129.12546877497877 chr12 133851895 35403689 0.2644989747810444 3.3632911749501053 chr13 115169878 60622713 0.5263764627761436 45.882910285563966 chr14 107349540 31533594 0.2937468944906518 21.542787200434997 chr15 102531392 14162918 0.13813250482349834 3.726512091322114 chr16 90354753 37590551 0.4160329119598169 47.36347502875562 chr17 81195210 10539043 0.1297988268027141 5.0137022000996625 chr18 78077248 18168056 0.23269334492937047 3.818473914678788 chr19 59128983 14224941 0.24057476178814036 57.48663001393126 chr20 63025520 7989475 0.12676571331739905 2.061329705776054 chr21 48129895 18893557 0.39255346391260565 21.94218083418382 chr22 51304566 3260434 0.06355056195193232 1.1566974927894529 chrMT 16571 507075 30.600144831331846 17.52388677535486 chrX 155270560 28287321 0.1821808396904088 2.5073816940774076 chrY 59373566 5092325 0.08576754510584728 1.4313862621196207