BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1770534.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 = 538,057,998 number of mapped reads = 519,143,331 (96.48%) number of supplementary alignments = 1,598,342 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 262,273,987 number of mapped paired reads (second in pair) = 256,869,344 number of mapped paired reads (both in pair) = 510,916,896 number of mapped paired reads (singletons) = 8,226,435 number of mapped bases = 51,612,025,523 bp number of sequenced bases = 51,597,145,308 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,773,479 duplication rate = 9.89% >>>>>>> Insert size mean insert size = 42,186.2973 std insert size = 1,960,183.0886 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 53.6039 >>>>>>> ACTG content number of A's = 15,235,844,631 bp (29.53%) number of C's = 10,554,871,476 bp (20.46%) number of T's = 15,222,601,104 bp (29.5%) number of G's = 10,567,412,457 bp (20.48%) number of N's = 16,415,640 bp (0.03%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 331,051,318 number of insertions = 5,122,493 mapped reads with insertion percentage = 0.96% number of deletions = 6,302,054 mapped reads with deletion percentage = 1.18% homopolymer indels = 42.78% >>>>>>> Coverage mean coverageData = 16.6722X std coverageData = 180.5209X There is a 91.72% of reference with a coverageData >= 1X There is a 91.66% of reference with a coverageData >= 2X There is a 91.6% of reference with a coverageData >= 3X There is a 91.51% of reference with a coverageData >= 4X There is a 91.37% of reference with a coverageData >= 5X There is a 91.13% of reference with a coverageData >= 6X There is a 90.73% of reference with a coverageData >= 7X There is a 90.04% of reference with a coverageData >= 8X There is a 88.92% of reference with a coverageData >= 9X There is a 87.17% of reference with a coverageData >= 10X There is a 84.61% of reference with a coverageData >= 11X There is a 81.09% of reference with a coverageData >= 12X There is a 76.52% of reference with a coverageData >= 13X There is a 70.93% of reference with a coverageData >= 14X There is a 64.44% of reference with a coverageData >= 15X There is a 57.29% of reference with a coverageData >= 16X There is a 49.78% of reference with a coverageData >= 17X There is a 42.26% of reference with a coverageData >= 18X There is a 35.03% of reference with a coverageData >= 19X There is a 28.35% of reference with a coverageData >= 20X There is a 22.43% of reference with a coverageData >= 21X There is a 17.36% of reference with a coverageData >= 22X There is a 13.16% of reference with a coverageData >= 23X There is a 9.79% of reference with a coverageData >= 24X There is a 7.18% of reference with a coverageData >= 25X There is a 5.2% of reference with a coverageData >= 26X There is a 3.74% of reference with a coverageData >= 27X There is a 2.69% of reference with a coverageData >= 28X There is a 1.96% of reference with a coverageData >= 29X There is a 1.45% of reference with a coverageData >= 30X There is a 1.11% of reference with a coverageData >= 31X There is a 0.87% of reference with a coverageData >= 32X There is a 0.71% of reference with a coverageData >= 33X There is a 0.61% of reference with a coverageData >= 34X There is a 0.53% of reference with a coverageData >= 35X There is a 0.48% of reference with a coverageData >= 36X There is a 0.44% of reference with a coverageData >= 37X There is a 0.41% of reference with a coverageData >= 38X There is a 0.38% of reference with a coverageData >= 39X There is a 0.36% of reference with a coverageData >= 40X There is a 0.35% of reference with a coverageData >= 41X There is a 0.33% of reference with a coverageData >= 42X There is a 0.31% of reference with a coverageData >= 43X There is a 0.3% of reference with a coverageData >= 44X There is a 0.29% of reference with a coverageData >= 45X There is a 0.28% of reference with a coverageData >= 46X There is a 0.27% of reference with a coverageData >= 47X There is a 0.26% of reference with a coverageData >= 48X There is a 0.25% of reference with a coverageData >= 49X There is a 0.24% of reference with a coverageData >= 50X There is a 0.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4198543535 16.844666296739135 454.8705257701876 chr2 243199373 4438225184 18.249328233259877 140.78890788794303 chr3 198022430 3388736525 17.112892337499343 17.876950295529674 chr4 191154276 3403242885 17.803645077759075 89.9838398533992 chr5 180915260 3102146835 17.146960599122483 13.62779108210732 chr6 171115067 2955663048 17.27295614476778 65.65790408159782 chr7 159138663 2800138137 17.595586667710034 149.63488147001271 chr8 146364022 2613217535 17.854234253005153 257.8315980212085 chr9 141213431 2170800021 15.372475589804202 184.5237510486844 chr10 135534747 2626333755 19.377567842436743 318.8608789527663 chr11 135006516 2330748252 17.26396859244927 70.43346564025647 chr12 133851895 2268776091 16.949898923732086 16.164368947426812 chr13 115169878 1651164229 14.33677153847467 10.877546948189492 chr14 107349540 1547041872 14.411257579678496 20.13772066223558 chr15 102531392 1434715960 13.992943351437187 11.433372571195848 chr16 90354753 1586483354 17.558382944171182 106.85309583686072 chr17 81195210 1414765749 17.424251369015487 99.50230989128126 chr18 78077248 1411816652 18.082305513636957 201.17174994373116 chr19 59128983 1045713964 17.685302722017052 232.37415415983858 chr20 63025520 1057459279 16.77827138911349 30.00914830865935 chr21 48129895 710002747 14.751803364624003 52.75895391399314 chr22 51304566 610671342 11.902865370696246 12.824469275183821 chrMT 16571 21362316 1289.138615653853 125.32724985162986 chrX 155270560 2675663548 17.23226571733882 46.44062084801933 chrY 59373566 148592708 2.5026744730137986 107.2548388744251