BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781883.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 120,869,322 number of mapped reads = 118,719,777 (98.22%) number of supplementary alignments = 406,244 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 59,769,116 number of mapped paired reads (second in pair) = 58,950,661 number of mapped paired reads (both in pair) = 117,533,840 number of mapped paired reads (singletons) = 1,185,937 number of mapped bases = 11,794,472,332 bp number of sequenced bases = 11,791,610,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,877,004 duplication rate = 4.75% >>>>>>> Insert size mean insert size = 48,687.2302 std insert size = 2,128,747.5093 median insert size = 278 >>>>>>> Mapping quality mean mapping quality = 54.0116 >>>>>>> ACTG content number of A's = 3,548,214,923 bp (30.09%) number of C's = 2,333,414,559 bp (19.79%) number of T's = 3,541,198,316 bp (30.03%) number of G's = 2,366,702,530 bp (20.07%) number of N's = 2,080,038 bp (0.02%) GC percentage = 39.86% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 42,001,933 number of insertions = 1,310,628 mapped reads with insertion percentage = 1.09% number of deletions = 1,277,648 mapped reads with deletion percentage = 1.06% homopolymer indels = 48.45% >>>>>>> Coverage mean coverageData = 3.81X std coverageData = 4.7242X There is a 81.55% of reference with a coverageData >= 1X There is a 67.91% of reference with a coverageData >= 2X There is a 54% of reference with a coverageData >= 3X There is a 41.74% of reference with a coverageData >= 4X There is a 31.76% of reference with a coverageData >= 5X There is a 23.98% of reference with a coverageData >= 6X There is a 18.08% of reference with a coverageData >= 7X There is a 13.66% of reference with a coverageData >= 8X There is a 10.36% of reference with a coverageData >= 9X There is a 7.9% of reference with a coverageData >= 10X There is a 6.06% of reference with a coverageData >= 11X There is a 4.67% of reference with a coverageData >= 12X There is a 3.63% of reference with a coverageData >= 13X There is a 2.84% of reference with a coverageData >= 14X There is a 2.23% of reference with a coverageData >= 15X There is a 1.77% of reference with a coverageData >= 16X There is a 1.41% of reference with a coverageData >= 17X There is a 1.13% of reference with a coverageData >= 18X There is a 0.91% of reference with a coverageData >= 19X There is a 0.74% of reference with a coverageData >= 20X There is a 0.6% of reference with a coverageData >= 21X There is a 0.49% of reference with a coverageData >= 22X There is a 0.41% of reference with a coverageData >= 23X There is a 0.34% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 906431309 3.6366260808634054 5.464154007386797 chr2 243199373 941698577 3.872125842199437 6.865848591773707 chr3 198022430 785861392 3.968547361023698 3.7075437471625037 chr4 191154276 745676132 3.9009126429376866 3.872296843411217 chr5 180915260 706222235 3.903607882497032 3.6328429160492393 chr6 171115067 660903098 3.8623314100096167 4.014615615584216 chr7 159138663 582571084 3.6607765392624922 3.9924853443507375 chr8 146364022 800878891 5.471828937578662 4.969018759033418 chr9 141213431 468117293 3.314962958445504 4.545764593086524 chr10 135534747 616632107 4.54962377286173 6.47313406829245 chr11 135006516 513630442 3.8044863108681364 3.7684862310482683 chr12 133851895 755487000 5.644201002906982 5.759192780248701 chr13 115169878 358566785 3.1133729689285596 3.4322906164793485 chr14 107349540 339868043 3.1659944048199926 3.6145026617094915 chr15 102531392 317183443 3.0935251810489417 3.7384741881792216 chr16 90354753 389722006 4.313243001173386 4.82862291404555 chr17 81195210 244095803 3.0062832893713805 3.6269799757511123 chr18 78077248 290034756 3.7147154059528327 4.062098935912874 chr19 59128983 159444954 2.6965617521275482 4.213795188071822 chr20 63025520 214331091 3.4007032548085285 4.189659316431891 chr21 48129895 134074725 2.785684967731594 4.792687083077924 chr22 51304566 99160816 1.9327873468416048 2.977088689953037 chrMT 16571 400126 24.1461589523867 8.945442488888427 chrX 155270560 753343754 4.851813209149243 4.614594910709129 chrY 59373566 10136470 0.17072361798177998 1.7270177877593946