BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472590.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 = 9,397,244 number of mapped reads = 8,632,775 (91.86%) number of supplementary alignments = 286,456 (3.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,359,950 number of mapped paired reads (second in pair) = 4,272,825 number of mapped paired reads (both in pair) = 8,419,890 number of mapped paired reads (singletons) = 212,885 number of mapped bases = 704,095,285 bp number of sequenced bases = 703,791,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,273,342 duplication rate = 12.55% >>>>>>> Insert size mean insert size = 242,863.771 std insert size = 4,692,751.8601 median insert size = 135 >>>>>>> Mapping quality mean mapping quality = 50.5593 >>>>>>> ACTG content number of A's = 184,913,695 bp (26.27%) number of C's = 136,828,238 bp (19.44%) number of T's = 213,676,560 bp (30.36%) number of G's = 167,931,306 bp (23.86%) number of N's = 441,433 bp (0.06%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.012 number of mismatches = 8,341,248 number of insertions = 66,830 mapped reads with insertion percentage = 0.76% number of deletions = 164,077 mapped reads with deletion percentage = 1.86% homopolymer indels = 43.34% >>>>>>> Coverage mean coverageData = 0.2274X std coverageData = 2.1053X There is a 12.96% of reference with a coverageData >= 1X There is a 5.51% of reference with a coverageData >= 2X There is a 1.89% of reference with a coverageData >= 3X There is a 0.86% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 42505037 0.17053131835527102 2.955270615382173 chr2 243199373 66650181 0.27405572710913195 3.168383170731747 chr3 198022430 35002420 0.1767598751313172 0.6121242738752671 chr4 191154276 34462189 0.18028468795539787 1.1013005288444024 chr5 180915260 31501328 0.17412200607068745 0.642249582611356 chr6 171115067 44576909 0.26050838059748416 1.203478567281323 chr7 159138663 62656256 0.3937211411660534 3.8334884841277863 chr8 146364022 33075364 0.22598015241751146 1.821520899604878 chr9 141213431 22947337 0.16250109382300895 2.3834441899567795 chr10 135534747 37049063 0.2733547213542222 2.1936954156394837 chr11 135006516 35255686 0.26114062524211795 2.0666779403736992 chr12 133851895 33640579 0.25132687886114724 0.7631449219817088 chr13 115169878 31831388 0.27638640027039013 0.8029451017265624 chr14 107349540 16496397 0.15366993654560607 3.502620360189246 chr15 102531392 19007715 0.18538434550854435 0.6444456666140441 chr16 90354753 23300573 0.25787877478896987 1.135094172204444 chr17 81195210 20060536 0.24706551039156127 1.8602196857211355 chr18 78077248 14920468 0.1910987948755571 3.6696731873716066 chr19 59128983 10676108 0.18055625952504545 2.011670832735484 chr20 63025520 25430140 0.40348957057395163 1.183088237624909 chr21 48129895 10184165 0.2115974904994079 0.8699343329247138 chr22 51304566 6084633 0.1185982744693718 0.5055152361599696 chrMT 16571 267966 16.170780278800315 10.103591407643446 chrX 155270560 44752027 0.2882196534874351 1.180477676541418 chrY 59373566 1760820 0.029656632043963807 0.8616006286099751