BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080949.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,561,113 number of mapped reads = 3,245,324 (91.13%) number of supplementary alignments = 35,024 (0.98%) number of secondary alignments = 0 number of mapped bases = 224,389,357 bp number of sequenced bases = 224,305,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,223 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8941 >>>>>>> ACTG content number of A's = 65,239,427 bp (29.09%) number of C's = 39,855,778 bp (17.77%) number of T's = 71,665,857 bp (31.95%) number of G's = 46,458,382 bp (20.71%) number of N's = 1,086,430 bp (0.48%) GC percentage = 38.48% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 2,532,690 number of insertions = 17,256 mapped reads with insertion percentage = 0.53% number of deletions = 50,217 mapped reads with deletion percentage = 1.53% homopolymer indels = 50.02% >>>>>>> Coverage mean coverageData = 0.0725X std coverageData = 0.5573X There is a 5.53% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% 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 17413966 0.0698652863135695 0.9293007816667542 chr2 243199373 19281262 0.0792817093323674 0.4935616397155297 chr3 198022430 15882716 0.08020665133742677 0.3522411768066306 chr4 191154276 16008759 0.08374784668693469 0.3741586442291112 chr5 180915260 14561771 0.08048945677661465 0.35299799917740776 chr6 171115067 13578745 0.07935446736551843 0.44619046484898506 chr7 159138663 12515986 0.07864830434072455 0.7026736934800414 chr8 146364022 11761434 0.08035741187817318 1.1607467190248164 chr9 141213431 9499339 0.06726937326521017 0.5019502814833356 chr10 135534747 9995682 0.07374995874674116 0.4861729760579269 chr11 135006516 10150965 0.0751887042252094 0.472032927720841 chr12 133851895 9991966 0.0746494175521385 0.3435510023271026 chr13 115169878 7919398 0.06876275409443432 0.32625101975596804 chr14 107349540 6841690 0.06373283015465181 0.3436261279891866 chr15 102531392 6027996 0.05879171132290879 0.3001977863977348 chr16 90354753 5368956 0.0594208475120285 0.3344000035941527 chr17 81195210 4780510 0.058876749010194074 0.3537642433593142 chr18 78077248 6204044 0.07946033138872928 0.9244713022068691 chr19 59128983 3288714 0.05561932293000879 0.6490073580639335 chr20 63025520 4171044 0.06618023936970294 0.33763927662775994 chr21 48129895 3021694 0.06278206092076452 0.34270485974705894 chr22 51304566 1866150 0.03637395548770454 0.23365086608415764 chrMT 16571 30528 1.8422545410657172 1.7347437858398391 chrX 155270560 13706658 0.08827596165042491 0.4054782748074257 chrY 59373566 519384 0.008747731271522414 0.1776320173298036