BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779334.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 = 141,092,640 number of mapped reads = 134,642,568 (95.43%) number of supplementary alignments = 578,084 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 68,183,792 number of mapped paired reads (second in pair) = 66,458,776 number of mapped paired reads (both in pair) = 131,960,934 number of mapped paired reads (singletons) = 2,681,634 number of mapped bases = 13,344,982,083 bp number of sequenced bases = 13,341,811,100 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,218,868 duplication rate = 5.78% >>>>>>> Insert size mean insert size = 58,948.8386 std insert size = 2,411,896.5535 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 54.0734 >>>>>>> ACTG content number of A's = 3,960,773,452 bp (29.69%) number of C's = 2,693,186,237 bp (20.19%) number of T's = 3,942,140,613 bp (29.55%) number of G's = 2,744,851,779 bp (20.57%) number of N's = 859,019 bp (0.01%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 46,994,697 number of insertions = 1,421,779 mapped reads with insertion percentage = 1.04% number of deletions = 1,432,634 mapped reads with deletion percentage = 1.05% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 4.3108X std coverageData = 7.4256X There is a 81.85% of reference with a coverageData >= 1X There is a 69.34% of reference with a coverageData >= 2X There is a 56.66% of reference with a coverageData >= 3X There is a 45.31% of reference with a coverageData >= 4X There is a 35.82% of reference with a coverageData >= 5X There is a 28.16% of reference with a coverageData >= 6X There is a 22.12% of reference with a coverageData >= 7X There is a 17.4% of reference with a coverageData >= 8X There is a 13.74% of reference with a coverageData >= 9X There is a 10.89% of reference with a coverageData >= 10X There is a 8.67% of reference with a coverageData >= 11X There is a 6.94% of reference with a coverageData >= 12X There is a 5.59% of reference with a coverageData >= 13X There is a 4.52% of reference with a coverageData >= 14X There is a 3.68% of reference with a coverageData >= 15X There is a 3.01% of reference with a coverageData >= 16X There is a 2.47% of reference with a coverageData >= 17X There is a 2.04% of reference with a coverageData >= 18X There is a 1.7% of reference with a coverageData >= 19X There is a 1.42% of reference with a coverageData >= 20X There is a 1.19% of reference with a coverageData >= 21X There is a 1% of reference with a coverageData >= 22X There is a 0.84% of reference with a coverageData >= 23X There is a 0.72% of reference with a coverageData >= 24X There is a 0.61% of reference with a coverageData >= 25X There is a 0.52% of reference with a coverageData >= 26X There is a 0.45% of reference with a coverageData >= 27X There is a 0.39% of reference with a coverageData >= 28X There is a 0.34% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.15% 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 0.05% 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 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1145359212 4.595211066695798 6.646163165824436 chr2 243199373 1115903223 4.588429687275551 19.39818840105392 chr3 198022430 961431402 4.855164144789052 4.85172748820494 chr4 191154276 823288686 4.306933139178116 4.679977844236188 chr5 180915260 819753235 4.531144774630952 4.46342941893968 chr6 171115067 790034551 4.61697829916988 4.965708697997878 chr7 159138663 685752765 4.309152484208065 4.748132431923992 chr8 146364022 656566605 4.485846972693877 4.590357878377754 chr9 141213431 544110892 3.8531100628806336 5.315303101685283 chr10 135534747 779588828 5.751948081623674 7.328342213692401 chr11 135006516 639140069 4.7341423802092635 5.004166481287806 chr12 133851895 608073911 4.542886083159301 6.2339035748669644 chr13 115169878 394270364 3.4233809295170046 4.019545213047267 chr14 107349540 392594897 3.6571642225947127 4.323921587694759 chr15 102531392 418875860 4.085342565133613 5.068351494443916 chr16 90354753 324511178 3.5915230491527104 4.508649674801458 chr17 81195210 333946009 4.112878198110455 5.501217227807135 chr18 78077248 349046029 4.470521668489135 5.363665828591755 chr19 59128983 210249082 3.5557703064163984 5.083036209936438 chr20 63025520 282601738 4.483925527310207 5.447649801137504 chr21 48129895 153593485 3.191228341553623 5.602538124095908 chr22 51304566 138757633 2.7045864299875375 4.155877517812057 chrMT 16571 819051 49.426769657835976 13.952578414955422 chrX 155270560 766309647 4.935318369432042 4.990053098521556 chrY 59373566 10403731 0.1752249645911448 2.142980783375666