BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472721.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 = 13,995,982 number of mapped reads = 13,824,920 (98.78%) number of supplementary alignments = 47,738 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,919,681 number of mapped paired reads (second in pair) = 6,905,239 number of mapped paired reads (both in pair) = 13,724,540 number of mapped paired reads (singletons) = 100,380 number of mapped bases = 1,359,780,492 bp number of sequenced bases = 1,359,614,997 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,256,439 duplication rate = 45.19% >>>>>>> Insert size mean insert size = 25,224.6449 std insert size = 1,551,249.1033 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 55.0867 >>>>>>> ACTG content number of A's = 379,601,706 bp (27.92%) number of C's = 306,110,813 bp (22.51%) number of T's = 371,040,150 bp (27.29%) number of G's = 302,600,555 bp (22.26%) number of N's = 261,773 bp (0.02%) GC percentage = 44.77% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 11,050,932 number of insertions = 76,524 mapped reads with insertion percentage = 0.54% number of deletions = 70,160 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.43% >>>>>>> Coverage mean coverageData = 0.4392X std coverageData = 14.1378X There is a 4.13% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 139478932 0.5595931173226646 16.799499046684314 chr2 243199373 95500444 0.39268375909834274 15.973343124870517 chr3 198022430 175093559 0.8842107381471886 21.597618979845784 chr4 191154276 56514846 0.2956504410081834 12.406939347463648 chr5 180915260 78327624 0.43295200194831546 13.270666122530658 chr6 171115067 87182450 0.5094960457222625 14.52751136240731 chr7 159138663 47649274 0.29941984620041706 9.302729410786322 chr8 146364022 54242422 0.3705994223088513 10.278265988315344 chr9 141213431 70256224 0.49751800166940213 11.507086462135153 chr10 135534747 28490253 0.2102062654088254 7.1689297133740135 chr11 135006516 65839743 0.48767826139591663 16.577806566663963 chr12 133851895 81378966 0.607977690566129 18.382742620625567 chr13 115169878 34722338 0.30148801581608 13.12040434684943 chr14 107349540 42228682 0.3933755282044059 13.760844812981874 chr15 102531392 50245206 0.4900470482249963 16.398700904783027 chr16 90354753 39951368 0.44216122200013097 12.232609893380237 chr17 81195210 48350437 0.5954838592079508 14.383285324499278 chr18 78077248 25493120 0.32651150819250185 13.058194760818052 chr19 59128983 24952365 0.42199888673884345 10.158847401330629 chr20 63025520 28708555 0.45550683278773424 13.710432352516051 chr21 48129895 4086503 0.08490571192810623 3.272002899622308 chr22 51304566 13365579 0.26051441503276723 10.108692595249076 chrMT 16571 3588 0.2165228411079597 0.735535433403343 chrX 155270560 64403549 0.4147827443914674 12.273019763551982 chrY 59373566 3314465 0.05582391665678292 3.720008313370572