BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781855.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 = 192,274,572 number of mapped reads = 187,529,174 (97.53%) number of supplementary alignments = 696,683 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 94,220,446 number of mapped paired reads (second in pair) = 93,308,728 number of mapped paired reads (both in pair) = 185,977,286 number of mapped paired reads (singletons) = 1,551,888 number of mapped bases = 18,622,795,916 bp number of sequenced bases = 18,618,976,275 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,746,638 duplication rate = 6.51% >>>>>>> Insert size mean insert size = 39,799.566 std insert size = 1,939,890.7332 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 53.9727 >>>>>>> ACTG content number of A's = 5,455,428,977 bp (29.3%) number of C's = 3,831,888,374 bp (20.58%) number of T's = 5,437,355,821 bp (29.2%) number of G's = 3,868,887,927 bp (20.78%) number of N's = 25,415,176 bp (0.14%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 101,842,276 number of insertions = 1,703,666 mapped reads with insertion percentage = 0.9% number of deletions = 1,696,859 mapped reads with deletion percentage = 0.89% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 6.0157X std coverageData = 7.4063X There is a 85.96% of reference with a coverageData >= 1X There is a 77.97% of reference with a coverageData >= 2X There is a 68.65% of reference with a coverageData >= 3X There is a 59.14% of reference with a coverageData >= 4X There is a 50.15% of reference with a coverageData >= 5X There is a 42.07% of reference with a coverageData >= 6X There is a 35.06% of reference with a coverageData >= 7X There is a 29.1% of reference with a coverageData >= 8X There is a 24.11% of reference with a coverageData >= 9X There is a 19.97% of reference with a coverageData >= 10X There is a 16.56% of reference with a coverageData >= 11X There is a 13.75% of reference with a coverageData >= 12X There is a 11.45% of reference with a coverageData >= 13X There is a 9.56% of reference with a coverageData >= 14X There is a 8% of reference with a coverageData >= 15X There is a 6.72% of reference with a coverageData >= 16X There is a 5.66% of reference with a coverageData >= 17X There is a 4.78% of reference with a coverageData >= 18X There is a 4.06% of reference with a coverageData >= 19X There is a 3.45% of reference with a coverageData >= 20X There is a 2.94% of reference with a coverageData >= 21X There is a 2.52% of reference with a coverageData >= 22X There is a 2.16% of reference with a coverageData >= 23X There is a 1.86% of reference with a coverageData >= 24X There is a 1.61% of reference with a coverageData >= 25X There is a 1.4% of reference with a coverageData >= 26X There is a 1.21% of reference with a coverageData >= 27X There is a 1.06% of reference with a coverageData >= 28X There is a 0.93% of reference with a coverageData >= 29X There is a 0.81% of reference with a coverageData >= 30X There is a 0.71% of reference with a coverageData >= 31X There is a 0.63% of reference with a coverageData >= 32X There is a 0.56% of reference with a coverageData >= 33X There is a 0.49% of reference with a coverageData >= 34X There is a 0.44% of reference with a coverageData >= 35X There is a 0.39% of reference with a coverageData >= 36X There is a 0.35% of reference with a coverageData >= 37X There is a 0.31% of reference with a coverageData >= 38X There is a 0.28% of reference with a coverageData >= 39X There is a 0.25% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1477340881 5.9271301915833545 10.465266861317824 chr2 243199373 1525253296 6.271616892696512 8.084976436452221 chr3 198022430 1268150448 6.404074770721681 5.837887490266162 chr4 191154276 1167798253 6.109192414822047 6.761252402106445 chr5 180915260 1113238186 6.153368079619154 5.52963018523512 chr6 171115067 1074923494 6.281875189868582 6.404306093923408 chr7 159138663 954457730 5.997648289906771 6.572942573926863 chr8 146364022 917487873 6.268534168868357 5.904432148358898 chr9 141213431 752365173 5.32785845986562 7.259798445746969 chr10 135534747 1030452350 7.602864747296131 11.701189629903322 chr11 135006516 846267787 6.268347721824034 6.118480524157301 chr12 133851895 1246802727 9.31479324218757 8.25121087478206 chr13 115169878 563083966 4.889160045823787 5.302468780336674 chr14 107349540 550680341 5.129787617161657 5.69853611311747 chr15 102531392 523865412 5.109317271338713 5.807766176325091 chr16 90354753 457687577 5.06545103388197 5.912282649906299 chr17 81195210 431238291 5.311129695951276 6.335083277374866 chr18 78077248 459001787 5.878816156532566 7.177557668588704 chr19 59128983 283503607 4.7946640144309605 7.4606928217879664 chr20 63025520 374763183 5.9462132640873095 6.898794830047511 chr21 48129895 214877136 4.464525343344298 9.582294597353178 chr22 51304566 183774479 3.58202969692795 5.259039025284399 chrMT 16571 1019153 61.502202643171806 18.347557120988345 chrX 155270560 1188345055 7.653382940075698 7.093861942334574 chrY 59373566 16417731 0.27651583197815677 3.02374958121365