BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779224.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 = 9,195,158 number of mapped reads = 8,966,537 (97.51%) number of supplementary alignments = 20,358 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,521,177 number of mapped paired reads (second in pair) = 4,445,360 number of mapped paired reads (both in pair) = 8,877,826 number of mapped paired reads (singletons) = 88,711 number of mapped bases = 713,628,098 bp number of sequenced bases = 713,493,439 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,194 duplication rate = 1.18% >>>>>>> Insert size mean insert size = 41,327.8213 std insert size = 1,897,955.8824 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 53.0999 >>>>>>> ACTG content number of A's = 217,440,590 bp (30.48%) number of C's = 138,413,472 bp (19.4%) number of T's = 216,553,254 bp (30.35%) number of G's = 140,950,459 bp (19.75%) number of N's = 135,664 bp (0.02%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 2,796,544 number of insertions = 50,626 mapped reads with insertion percentage = 0.56% number of deletions = 64,449 mapped reads with deletion percentage = 0.71% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.2305X std coverageData = 0.8251X There is a 15.81% of reference with a coverageData >= 1X There is a 4.5% of reference with a coverageData >= 2X There is a 1.39% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% of reference with a coverageData >= 18X There is a 0.01% 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% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% 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 49889549 0.2001581733270787 0.9744556349168038 chr2 243199373 55352670 0.22760202593120996 0.6077153823350004 chr3 198022430 45820891 0.2313924286253835 0.6069140224759171 chr4 191154276 48005828 0.25113656364140136 0.6362741397983499 chr5 180915260 43959701 0.24298503619871537 0.625144940791876 chr6 171115067 37664212 0.22011043597931676 0.6177923799424481 chr7 159138663 81718338 0.5135039873999695 2.203290398028459 chr8 146364022 54198227 0.37029746968828176 0.792872428551699 chr9 141213431 29092078 0.20601495051841068 0.625747004300671 chr10 135534747 14504901 0.10701979618554938 0.9030341379391471 chr11 135006516 24567760 0.18197462409888424 0.5403161369613765 chr12 133851895 34590224 0.2584216233920334 0.6499858508626423 chr13 115169878 27625107 0.239863994646239 0.6301935604705622 chr14 107349540 20523449 0.19118339025952044 0.5613724423333605 chr15 102531392 16877820 0.16461124413486944 0.5204756171806328 chr16 90354753 15152691 0.1677022015654229 0.51541936544898 chr17 81195210 11335902 0.13961294022147366 0.5061243135657498 chr18 78077248 20702473 0.26515372314352065 0.6775005118531477 chr19 59128983 6731764 0.11384880406280622 0.6258384096660967 chr20 63025520 14800982 0.234841092941399 0.6293891250541741 chr21 48129895 9644838 0.20039183546941045 0.5826969966642572 chr22 51304566 4583752 0.08934393870518269 0.3694575898057296 chrMT 16571 8469 0.5110735622472995 0.7277659185704376 chrX 155270560 45834108 0.29518865649740683 0.7274341459085552 chrY 59373566 442364 0.007450520994477576 0.11437610672995141