BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084967.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 = 2,611,932 number of mapped reads = 2,343,309 (89.72%) number of supplementary alignments = 22,025 (0.84%) number of secondary alignments = 0 number of mapped bases = 154,937,149 bp number of sequenced bases = 154,879,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,904 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5067 >>>>>>> ACTG content number of A's = 43,030,244 bp (27.78%) number of C's = 29,401,534 bp (18.98%) number of T's = 47,445,921 bp (30.63%) number of G's = 34,981,291 bp (22.59%) number of N's = 20,332 bp (0.01%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,331,375 number of insertions = 12,310 mapped reads with insertion percentage = 0.52% number of deletions = 36,128 mapped reads with deletion percentage = 1.53% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.05X std coverageData = 0.5118X There is a 4.36% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 12415924 0.04981301129837506 1.1262490943220924 chr2 243199373 12664250 0.05207353063365011 0.6332448235981021 chr3 198022430 10514528 0.05309766171438256 0.26126208432309356 chr4 191154276 10188691 0.05330087933790192 0.26434033045201577 chr5 180915260 10167292 0.05619919513699397 0.2666186195200729 chr6 171115067 8679005 0.05072028519849745 0.3336220606910332 chr7 159138663 8270852 0.05197261208610254 0.4082364317956719 chr8 146364022 7232502 0.04941447974147636 0.5545425720610019 chr9 141213431 6886155 0.04876416464946596 0.4700390646540521 chr10 135534747 7679066 0.056657544799194555 0.5170775291095071 chr11 135006516 6827879 0.05057444042182379 0.4682817124033852 chr12 133851895 7100884 0.05305030608643979 0.261149966936617 chr13 115169878 4254815 0.03694381789655104 0.21158719028870654 chr14 107349540 5082480 0.047345149313168924 0.26962346837955425 chr15 102531392 4292337 0.041863637236096436 0.23098756109008248 chr16 90354753 4614882 0.05107514377245877 0.30131042791977286 chr17 81195210 4256703 0.05242554332946488 0.30510356505559366 chr18 78077248 3813193 0.048838721877082554 0.9067417127726977 chr19 59128983 3200236 0.05412296707352467 0.7315855278424799 chr20 63025520 3295098 0.052281964512153174 0.2688537265413605 chr21 48129895 1901118 0.03949973296222649 0.23765226630086972 chr22 51304566 1637047 0.031908407528483916 0.1965009865502896 chrMT 16571 14407 0.8694104157866152 1.0274243103414922 chrX 155270560 9561907 0.0615822278221963 0.3609747391269793 chrY 59373566 385898 0.006499491709829253 0.12174390522095696