BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781824.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 = 174,558,694 number of mapped reads = 168,665,524 (96.62%) number of supplementary alignments = 583,169 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 84,990,244 number of mapped paired reads (second in pair) = 83,675,280 number of mapped paired reads (both in pair) = 166,492,758 number of mapped paired reads (singletons) = 2,172,766 number of mapped bases = 16,735,448,254 bp number of sequenced bases = 16,731,995,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,548,710 duplication rate = 6.58% >>>>>>> Insert size mean insert size = 42,626.2075 std insert size = 2,010,552.6765 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 53.905 >>>>>>> ACTG content number of A's = 4,981,463,262 bp (29.77%) number of C's = 3,377,944,047 bp (20.19%) number of T's = 4,964,768,685 bp (29.67%) number of G's = 3,406,367,798 bp (20.36%) number of N's = 1,452,009 bp (0.01%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 78,033,636 number of insertions = 1,855,086 mapped reads with insertion percentage = 1.08% number of deletions = 1,561,684 mapped reads with deletion percentage = 0.91% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 5.406X std coverageData = 6.9745X There is a 83.48% of reference with a coverageData >= 1X There is a 73.49% of reference with a coverageData >= 2X There is a 62.89% of reference with a coverageData >= 3X There is a 52.87% of reference with a coverageData >= 4X There is a 43.96% of reference with a coverageData >= 5X There is a 36.33% of reference with a coverageData >= 6X There is a 29.94% of reference with a coverageData >= 7X There is a 24.66% of reference with a coverageData >= 8X There is a 20.35% of reference with a coverageData >= 9X There is a 16.83% of reference with a coverageData >= 10X There is a 13.96% of reference with a coverageData >= 11X There is a 11.63% of reference with a coverageData >= 12X There is a 9.72% of reference with a coverageData >= 13X There is a 8.15% of reference with a coverageData >= 14X There is a 6.87% of reference with a coverageData >= 15X There is a 5.81% of reference with a coverageData >= 16X There is a 4.93% of reference with a coverageData >= 17X There is a 4.2% of reference with a coverageData >= 18X There is a 3.59% of reference with a coverageData >= 19X There is a 3.08% of reference with a coverageData >= 20X There is a 2.65% of reference with a coverageData >= 21X There is a 2.29% of reference with a coverageData >= 22X There is a 1.99% of reference with a coverageData >= 23X There is a 1.73% of reference with a coverageData >= 24X There is a 1.5% of reference with a coverageData >= 25X There is a 1.31% of reference with a coverageData >= 26X There is a 1.15% of reference with a coverageData >= 27X There is a 1.01% of reference with a coverageData >= 28X There is a 0.89% of reference with a coverageData >= 29X There is a 0.79% of reference with a coverageData >= 30X There is a 0.7% of reference with a coverageData >= 31X There is a 0.62% of reference with a coverageData >= 32X There is a 0.55% 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 0.32% of reference with a coverageData >= 38X There is a 0.29% of reference with a coverageData >= 39X There is a 0.26% 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 0.18% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% 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 0.11% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1325082550 5.3162657917710865 8.696698313781052 chr2 243199373 1380392255 5.6759696292473585 9.038407873443328 chr3 198022430 1149148969 5.8031252772728825 5.776285636079745 chr4 191154276 1083519698 5.668299557159789 5.913093788167112 chr5 180915260 1024086575 5.660587033951696 5.508027094024951 chr6 171115067 983701002 5.748769054919051 5.937899503327168 chr7 159138663 853219046 5.361481804079252 6.480758382185899 chr8 146364022 843055625 5.759992199449124 5.8330844711436765 chr9 141213431 682528655 4.833312597581458 6.92410962729312 chr10 135534747 906742158 6.690108463477635 10.381063279807385 chr11 135006516 757752860 5.61271324118904 5.954340301314572 chr12 133851895 1111069191 8.300735607814891 8.162276989596068 chr13 115169878 530646837 4.6075141019077925 5.328615682475494 chr14 107349540 492640831 4.589128476936184 5.565193984319145 chr15 102531392 458621046 4.4729817576259965 5.5633318846807205 chr16 90354753 378559124 4.1896979564539345 5.457885156125909 chr17 81195210 341738717 4.20885317003306 5.329504272641932 chr18 78077248 414314682 5.306471380753584 6.167114313922804 chr19 59128983 224548088 3.7975976688115876 6.123983993302703 chr20 63025520 304855359 4.8370145775869835 6.472266686168191 chr21 48129895 190628685 3.960712671407241 7.01371359531575 chr22 51304566 136258948 2.655883454895613 4.327495926770173 chrMT 16571 592030 35.72687224669603 10.807182724831732 chrX 155270560 1146016673 7.3807724593767166 7.666105850161153 chrY 59373566 15728650 0.26490997694159046 2.6371653433388293