BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779220.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 = 11,378,630 number of mapped reads = 11,020,108 (96.85%) number of supplementary alignments = 28,554 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,564,729 number of mapped paired reads (second in pair) = 5,455,379 number of mapped paired reads (both in pair) = 10,893,870 number of mapped paired reads (singletons) = 126,238 number of mapped bases = 876,843,241 bp number of sequenced bases = 876,675,691 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 173,780 duplication rate = 1.4% >>>>>>> Insert size mean insert size = 50,899.3878 std insert size = 2,154,796.4447 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.0275 >>>>>>> ACTG content number of A's = 266,459,044 bp (30.39%) number of C's = 170,851,410 bp (19.49%) number of T's = 265,082,285 bp (30.24%) number of G's = 174,117,055 bp (19.86%) number of N's = 165,897 bp (0.02%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 3,337,557 number of insertions = 63,747 mapped reads with insertion percentage = 0.57% number of deletions = 80,476 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.2832X std coverageData = 0.9438X There is a 17.39% of reference with a coverageData >= 1X There is a 6.08% of reference with a coverageData >= 2X There is a 2.34% of reference with a coverageData >= 3X There is a 1.01% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 60728555 0.2436445484322384 0.8036014311381943 chr2 243199373 73931368 0.30399489557894543 0.7922375257569262 chr3 198022430 82710648 0.41768322911702477 0.9334767407550263 chr4 191154276 51347606 0.26861866276012575 0.7220419001832746 chr5 180915260 38127519 0.21074794353997556 0.6270846802251263 chr6 171115067 67884360 0.39671760757338803 0.9174497923219896 chr7 159138663 80873554 0.508195509974845 2.421173217163138 chr8 146364022 65034101 0.44433119636463664 0.9583940375432597 chr9 141213431 32747678 0.23190200654497234 0.7454932292479275 chr10 135534747 12382940 0.09136358221113587 0.948968831635401 chr11 135006516 46236201 0.34247384770672845 0.8584774663030837 chr12 133851895 44474239 0.3322645450779759 0.8147089195170746 chr13 115169878 28201042 0.2448647379829646 0.6723446979421631 chr14 107349540 37924328 0.35327890552674934 0.8605035774292461 chr15 102531392 21286701 0.2076115478857441 0.6382352568755456 chr16 90354753 22565209 0.24974014371994355 0.7114966550301761 chr17 81195210 14282699 0.17590568458410294 0.585328616500757 chr18 78077248 23150024 0.2965015365295662 0.8059105257202923 chr19 59128983 10909099 0.18449664524079504 0.7210696140784092 chr20 63025520 25898822 0.41092595507343693 0.9751315983080505 chr21 48129895 8680590 0.18035755116440624 0.6011270304169211 chr22 51304566 6938964 0.13525041806220522 0.48727127462654196 chrMT 16571 2416 0.1457968740570877 0.41730669384651575 chrX 155270560 20056709 0.12917264547767457 0.5211617350460461 chrY 59373566 467869 0.007880089263966392 0.14319827635253257