BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779382.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 = 16,215,850 number of mapped reads = 15,561,641 (95.97%) number of supplementary alignments = 64,305 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,824,623 number of mapped paired reads (second in pair) = 7,737,018 number of mapped paired reads (both in pair) = 15,444,398 number of mapped paired reads (singletons) = 117,243 number of mapped bases = 1,236,733,778 bp number of sequenced bases = 1,236,463,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 746,282 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 123,389.513 std insert size = 3,244,387.3429 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 46.2185 >>>>>>> ACTG content number of A's = 373,484,944 bp (30.21%) number of C's = 244,493,891 bp (19.77%) number of T's = 368,949,521 bp (29.84%) number of G's = 249,263,496 bp (20.16%) number of N's = 271,740 bp (0.02%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 3,975,479 number of insertions = 110,657 mapped reads with insertion percentage = 0.7% number of deletions = 129,637 mapped reads with deletion percentage = 0.82% homopolymer indels = 47.24% >>>>>>> Coverage mean coverageData = 0.3995X std coverageData = 1.6941X There is a 13.94% of reference with a coverageData >= 1X There is a 7.97% of reference with a coverageData >= 2X There is a 4.99% of reference with a coverageData >= 3X There is a 3.35% of reference with a coverageData >= 4X There is a 2.34% of reference with a coverageData >= 5X There is a 1.68% of reference with a coverageData >= 6X There is a 1.23% of reference with a coverageData >= 7X There is a 0.92% of reference with a coverageData >= 8X There is a 0.69% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 0.01% 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 62651524 0.2513595502736982 2.1820514135613607 chr2 243199373 100534916 0.41338476641549565 1.4049516308491965 chr3 198022430 6542078 0.033037055448718614 0.4105997925300556 chr4 191154276 11641975 0.060903555199570844 0.5381543100245283 chr5 180915260 170536814 0.9426336617485999 2.0862569605819044 chr6 171115067 118082917 0.6900790156602633 2.1797108643495426 chr7 159138663 213132739 1.339289491203027 3.3363406753576514 chr8 146364022 49009033 0.3348434426050413 1.356544432513189 chr9 141213431 89789229 0.6358405738332354 2.099116990227003 chr10 135534747 63484558 0.46840060873836287 1.6256574953648075 chr11 135006516 62526034 0.4631334534993852 1.652255226438205 chr12 133851895 45746370 0.341768564427123 1.2857098626442196 chr13 115169878 493206 0.004282421832555905 0.10131103863928852 chr14 107349540 14003342 0.1304462226852579 0.7012525927818175 chr15 102531392 25078346 0.24459188069932766 1.1865251203233065 chr16 90354753 21572386 0.23875208866986777 1.0661799766409927 chr17 81195210 43531268 0.5361309860520097 2.367527789122378 chr18 78077248 51360951 0.6578222505998162 1.9479708166335403 chr19 59128983 2171639 0.0367271495266543 1.5744017082909776 chr20 63025520 4259437 0.06758273473983237 0.5775244041611465 chr21 48129895 22163187 0.4604869177462365 1.513739759060293 chr22 51304566 10361190 0.20195453948484818 0.959133336576282 chrMT 16571 823 0.049665077545108925 0.29459410775130856 chrX 155270560 47234456 0.304207417040294 1.1369144006444127 chrY 59373566 825360 0.013901135734377146 0.20193519539559773