BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781808.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 = 149,018,470 number of mapped reads = 146,320,497 (98.19%) number of supplementary alignments = 531,691 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 73,632,300 number of mapped paired reads (second in pair) = 72,688,197 number of mapped paired reads (both in pair) = 144,865,298 number of mapped paired reads (singletons) = 1,455,199 number of mapped bases = 14,534,598,926 bp number of sequenced bases = 14,531,584,166 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,307,952 duplication rate = 5.44% >>>>>>> Insert size mean insert size = 38,434.0592 std insert size = 1,909,236.5719 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 54.006 >>>>>>> ACTG content number of A's = 4,281,766,645 bp (29.47%) number of C's = 2,968,317,869 bp (20.43%) number of T's = 4,270,556,476 bp (29.39%) number of G's = 3,009,564,158 bp (20.71%) number of N's = 1,379,018 bp (0.01%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 63,213,505 number of insertions = 1,325,569 mapped reads with insertion percentage = 0.89% number of deletions = 1,336,266 mapped reads with deletion percentage = 0.9% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 4.6951X std coverageData = 5.6797X There is a 83.55% of reference with a coverageData >= 1X There is a 72.78% of reference with a coverageData >= 2X There is a 61.08% of reference with a coverageData >= 3X There is a 49.99% of reference with a coverageData >= 4X There is a 40.24% of reference with a coverageData >= 5X There is a 32.07% of reference with a coverageData >= 6X There is a 25.42% of reference with a coverageData >= 7X There is a 20.1% of reference with a coverageData >= 8X There is a 15.9% of reference with a coverageData >= 9X There is a 12.59% of reference with a coverageData >= 10X There is a 10% of reference with a coverageData >= 11X There is a 7.98% of reference with a coverageData >= 12X There is a 6.39% of reference with a coverageData >= 13X There is a 5.14% of reference with a coverageData >= 14X There is a 4.16% of reference with a coverageData >= 15X There is a 3.37% of reference with a coverageData >= 16X There is a 2.75% of reference with a coverageData >= 17X There is a 2.26% of reference with a coverageData >= 18X There is a 1.86% of reference with a coverageData >= 19X There is a 1.54% of reference with a coverageData >= 20X There is a 1.28% of reference with a coverageData >= 21X There is a 1.07% of reference with a coverageData >= 22X There is a 0.9% of reference with a coverageData >= 23X There is a 0.76% of reference with a coverageData >= 24X There is a 0.64% of reference with a coverageData >= 25X There is a 0.55% of reference with a coverageData >= 26X There is a 0.47% of reference with a coverageData >= 27X There is a 0.4% of reference with a coverageData >= 28X There is a 0.35% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1145278246 4.5948862289895755 8.115955065416697 chr2 243199373 1199964127 4.934075742867972 5.429850667864102 chr3 198022430 999838080 5.049115294666366 4.655110611746168 chr4 191154276 921394052 4.820159251891389 5.277552894536546 chr5 180915260 880775353 4.868441462594145 4.439620654399196 chr6 171115067 842674131 4.924605096288803 5.092709178585217 chr7 159138663 732548568 4.603209265368781 5.165248937592281 chr8 146364022 715271168 4.886932992316924 4.644016178319776 chr9 141213431 591715140 4.19021856355859 5.713586330993149 chr10 135534747 803918883 5.9314596499744825 8.495014583270773 chr11 135006516 657288660 4.868569899248419 4.8127144477127315 chr12 133851895 955782386 7.140596597455718 6.357724733837722 chr13 115169878 450310133 3.9099644874157113 4.261805710350324 chr14 107349540 430543955 4.01067349706389 4.49987450064602 chr15 102531392 408059931 3.979853614003407 4.556190031747537 chr16 90354753 355227322 3.9314735551321798 4.653263615288245 chr17 81195210 331255749 4.07974496278783 5.125027566961167 chr18 78077248 365298902 4.678685678060784 5.7220697130642515 chr19 59128983 214703964 3.631112072399419 5.748642152244091 chr20 63025520 286624677 4.547755845568589 5.32399218670554 chr21 48129895 169945974 3.530985762591005 6.977232069646545 chr22 51304566 137721494 2.684390586210202 4.014165022718855 chrMT 16571 620882 37.467986241023475 11.037113128594848 chrX 155270560 924709872 5.9554745729003615 5.591764791831657 chrY 59373566 13127277 0.22109632087788023 2.452213227359282