BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082967.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 = 3,391,281 number of mapped reads = 2,895,130 (85.37%) number of supplementary alignments = 17,465 (0.51%) number of secondary alignments = 0 number of mapped bases = 196,853,541 bp number of sequenced bases = 196,766,129 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 162,230 duplication rate = 4.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2666 >>>>>>> ACTG content number of A's = 55,895,742 bp (28.41%) number of C's = 35,552,763 bp (18.07%) number of T's = 64,308,893 bp (32.68%) number of G's = 40,989,175 bp (20.83%) number of N's = 19,556 bp (0.01%) GC percentage = 38.9% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,812,090 number of insertions = 16,922 mapped reads with insertion percentage = 0.58% number of deletions = 50,375 mapped reads with deletion percentage = 1.72% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.0636X std coverageData = 0.6441X There is a 4.87% of reference with a coverageData >= 1X There is a 0.99% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% 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 0.01% 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 15558126 0.06241960777301333 1.289134700151328 chr2 243199373 16697310 0.06865687930864854 0.706401092792951 chr3 198022430 13437529 0.0678586208643132 0.3294083931618766 chr4 191154276 14565637 0.07619833207393174 0.357481923372896 chr5 180915260 12460245 0.0688733775138703 0.3356667932997763 chr6 171115067 11882166 0.06943962450717446 0.4155867034316986 chr7 159138663 11116407 0.0698535905130735 0.7760139960486065 chr8 146364022 10105627 0.06904447460455822 0.9508113055455464 chr9 141213431 8931051 0.0632450535105262 0.682748931315442 chr10 135534747 9039886 0.06669792212029584 0.44665413650120617 chr11 135006516 8649968 0.06407074455576647 0.4838262316079991 chr12 133851895 8598252 0.06423705842939317 0.33489274270069086 chr13 115169878 6542552 0.05680783998051991 0.29771143719059584 chr14 107349540 5763932 0.05369312248566691 0.354946614593155 chr15 102531392 5287600 0.051570547291506584 0.2829547087052098 chr16 90354753 4834905 0.053510245332639005 0.39552962919928475 chr17 81195210 4341500 0.053469902965950826 0.36649618102115405 chr18 78077248 5410498 0.0692967303355774 1.3831552345076363 chr19 59128983 3012970 0.050955890785403836 0.7731550586830297 chr20 63025520 3607633 0.05724082879443121 0.3201458374565763 chr21 48129895 2609076 0.05420905239872225 0.3434410047269594 chr22 51304566 1787458 0.03484013489169755 0.2269592517245946 chrMT 16571 20627 1.2447649508176937 1.4588708597867592 chrX 155270560 12125137 0.07809037978609724 0.41231470400390535 chrY 59373566 467449 0.007873015408911097 0.1876475948423138