BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472446.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 30,189,822 number of mapped reads = 27,393,709 (90.74%) number of supplementary alignments = 171,964 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,748,144 number of mapped paired reads (second in pair) = 13,645,565 number of mapped paired reads (both in pair) = 27,244,204 number of mapped paired reads (singletons) = 149,505 number of mapped bases = 2,682,003,855 bp number of sequenced bases = 2,681,739,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,370,037 duplication rate = 33.62% >>>>>>> Insert size mean insert size = 16,069.1333 std insert size = 1,093,052.5052 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 48.1527 >>>>>>> ACTG content number of A's = 704,014,877 bp (26.25%) number of C's = 637,883,185 bp (23.79%) number of T's = 705,063,516 bp (26.29%) number of G's = 634,463,777 bp (23.66%) number of N's = 314,295 bp (0.01%) GC percentage = 47.44% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 14,694,796 number of insertions = 110,937 mapped reads with insertion percentage = 0.4% number of deletions = 144,557 mapped reads with deletion percentage = 0.53% homopolymer indels = 55.14% >>>>>>> Coverage mean coverageData = 0.8664X std coverageData = 296.5479X There is a 1.04% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.08% of reference with a coverageData >= 29X There is a 0.07% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% 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 112061845 0.44959504835095276 131.36613041488891 chr2 243199373 360120800 1.4807636860149307 298.34278229065785 chr3 198022430 614043586 3.1008789559849355 761.964367352306 chr4 191154276 6505147 0.03403087357564526 1.0810873356633786 chr5 180915260 3277258 0.018114878755943527 0.4894552391710753 chr6 171115067 11572568 0.06763032737497043 2.31936163539737 chr7 159138663 145346112 0.9133299806596967 133.15082032601845 chr8 146364022 332029630 2.2685194453046664 242.91169480736332 chr9 141213431 139892642 0.9906468599293505 97.10692487031018 chr10 135534747 2600896 0.01918988346213536 4.352068072615737 chr11 135006516 2566470 0.019009971340938833 0.5687278069707798 chr12 133851895 9267018 0.06923337170534642 1.7420492983784563 chr13 115169878 778618663 6.760610296035913 1011.5197487701105 chr14 107349540 1405019 0.013088262884032852 0.38731203464659 chr15 102531392 8107562 0.07907394839621411 4.597077126763373 chr16 90354753 11605724 0.12844619253178635 6.948334788839949 chr17 81195210 18228042 0.22449651894489836 3.8413029571713495 chr18 78077248 31368980 0.4017685152017653 22.097515311133968 chr19 59128983 40331020 0.6820854672910576 64.79106660103568 chr20 63025520 3370086 0.05347176826149153 1.3572568262477704 chr21 48129895 17674510 0.36722519340630183 69.53732482590699 chr22 51304566 2348518 0.0457760036406896 8.195342977165057 chrMT 16571 2428 0.14652103071631162 0.4629959750492019 chrX 155270560 29305451 0.18873797453941044 31.088922517141057 chrY 59373566 353880 0.005960228159447253 1.9637686440086493