BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779345.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 = 304,893,820 number of mapped reads = 272,562,416 (89.4%) number of supplementary alignments = 1,650,642 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 138,135,067 number of mapped paired reads (second in pair) = 134,427,349 number of mapped paired reads (both in pair) = 265,157,444 number of mapped paired reads (singletons) = 7,404,972 number of mapped bases = 27,289,206,802 bp number of sequenced bases = 27,281,829,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,090,887 duplication rate = 10.75% >>>>>>> Insert size mean insert size = 52,071.5027 std insert size = 2,212,467.0986 median insert size = 313 >>>>>>> Mapping quality mean mapping quality = 53.9038 >>>>>>> ACTG content number of A's = 8,204,294,557 bp (30.07%) number of C's = 5,403,870,959 bp (19.81%) number of T's = 8,134,848,641 bp (29.82%) number of G's = 5,533,099,707 bp (20.28%) number of N's = 5,715,382 bp (0.02%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 114,612,010 number of insertions = 2,741,651 mapped reads with insertion percentage = 0.99% number of deletions = 3,322,103 mapped reads with deletion percentage = 1.2% homopolymer indels = 48.09% >>>>>>> Coverage mean coverageData = 8.8152X std coverageData = 31.5245X There is a 82.41% of reference with a coverageData >= 1X There is a 74.87% of reference with a coverageData >= 2X There is a 67.98% of reference with a coverageData >= 3X There is a 61.62% of reference with a coverageData >= 4X There is a 55.73% of reference with a coverageData >= 5X There is a 50.31% of reference with a coverageData >= 6X There is a 45.35% of reference with a coverageData >= 7X There is a 40.84% of reference with a coverageData >= 8X There is a 36.74% of reference with a coverageData >= 9X There is a 33.04% of reference with a coverageData >= 10X There is a 29.69% of reference with a coverageData >= 11X There is a 26.68% of reference with a coverageData >= 12X There is a 23.97% of reference with a coverageData >= 13X There is a 21.54% of reference with a coverageData >= 14X There is a 19.36% of reference with a coverageData >= 15X There is a 17.4% of reference with a coverageData >= 16X There is a 15.65% of reference with a coverageData >= 17X There is a 14.09% of reference with a coverageData >= 18X There is a 12.68% of reference with a coverageData >= 19X There is a 11.42% of reference with a coverageData >= 20X There is a 10.3% of reference with a coverageData >= 21X There is a 9.29% of reference with a coverageData >= 22X There is a 8.38% of reference with a coverageData >= 23X There is a 7.57% of reference with a coverageData >= 24X There is a 6.85% of reference with a coverageData >= 25X There is a 6.19% of reference with a coverageData >= 26X There is a 5.61% of reference with a coverageData >= 27X There is a 5.08% of reference with a coverageData >= 28X There is a 4.61% of reference with a coverageData >= 29X There is a 4.18% of reference with a coverageData >= 30X There is a 3.8% of reference with a coverageData >= 31X There is a 3.46% of reference with a coverageData >= 32X There is a 3.15% of reference with a coverageData >= 33X There is a 2.86% of reference with a coverageData >= 34X There is a 2.61% of reference with a coverageData >= 35X There is a 2.38% of reference with a coverageData >= 36X There is a 2.18% of reference with a coverageData >= 37X There is a 1.99% of reference with a coverageData >= 38X There is a 1.82% of reference with a coverageData >= 39X There is a 1.67% of reference with a coverageData >= 40X There is a 1.53% of reference with a coverageData >= 41X There is a 1.4% of reference with a coverageData >= 42X There is a 1.29% of reference with a coverageData >= 43X There is a 1.19% of reference with a coverageData >= 44X There is a 1.09% of reference with a coverageData >= 45X There is a 1.01% of reference with a coverageData >= 46X There is a 0.93% of reference with a coverageData >= 47X There is a 0.86% of reference with a coverageData >= 48X There is a 0.79% of reference with a coverageData >= 49X There is a 0.73% of reference with a coverageData >= 50X There is a 0.68% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2057972910 8.256641053664616 71.44062270212805 chr2 243199373 2081127334 8.557289060116121 16.876179042744926 chr3 198022430 1727206914 8.722279157972155 9.336721511765074 chr4 191154276 1581825953 8.275127222369852 11.11885979864345 chr5 180915260 1733548931 9.582104522305084 10.03426060327332 chr6 171115067 1522809194 8.899328508576044 13.4272402930463 chr7 159138663 2670443785 16.78060965612109 63.674463029134586 chr8 146364022 1977189995 13.508715926103752 14.340788894865563 chr9 141213431 1058399173 7.495031920865941 20.51861320462864 chr10 135534747 718320533 5.299899464157336 61.3153928932861 chr11 135006516 1283918399 9.510047640959788 11.203182580900545 chr12 133851895 1175932720 8.785327394879243 22.870420499008837 chr13 115169878 815610515 7.081804106799523 9.07466319365853 chr14 107349540 908362598 8.461727903072523 10.474077329281524 chr15 102531392 659693410 6.434062750264816 10.361473621961837 chr16 90354753 689367020 7.6295601184367134 10.628035855301263 chr17 81195210 639835835 7.8802165176985195 22.029753368916612 chr18 78077248 760557079 9.741084611486306 22.891614702410077 chr19 59128983 471565762 7.975205019169702 46.410149860009895 chr20 63025520 696509232 11.051225471840613 12.46050374567045 chr21 48129895 391435750 8.132902637747287 11.475935784447582 chr22 51304566 244877206 4.773009989013453 8.050648307691025 chrMT 16571 48935 2.953050509926981 2.5864186453046063 chrX 155270560 1402865273 9.034972714724542 11.620040353828777 chrY 59373566 19782346 0.33318440061356597 4.170017527294333