BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085050.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 = 2,051,077 number of mapped reads = 1,847,033 (90.05%) number of supplementary alignments = 11,698 (0.57%) number of secondary alignments = 0 number of mapped bases = 124,049,701 bp number of sequenced bases = 124,005,577 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,871 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7351 >>>>>>> ACTG content number of A's = 35,921,767 bp (28.97%) number of C's = 23,541,810 bp (18.98%) number of T's = 37,980,086 bp (30.63%) number of G's = 26,548,059 bp (21.41%) number of N's = 13,855 bp (0.01%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,115,377 number of insertions = 9,048 mapped reads with insertion percentage = 0.49% number of deletions = 25,914 mapped reads with deletion percentage = 1.39% homopolymer indels = 45.61% >>>>>>> Coverage mean coverageData = 0.0401X std coverageData = 0.3399X There is a 3.51% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 13182352 0.052887940447699025 0.4936448996543361 chr2 243199373 13062961 0.053712971537965275 0.4211589795216172 chr3 198022430 8022332 0.040512238941820884 0.2276256944747534 chr4 191154276 8077253 0.042255152063666104 0.2344212075877076 chr5 180915260 5518104 0.030501042311190333 0.19369586142623038 chr6 171115067 6572761 0.038411351584837355 0.29183162171082233 chr7 159138663 9205254 0.0578442336165662 0.45111322999325054 chr8 146364022 7639668 0.052196351914953525 0.5864346688147137 chr9 141213431 4689310 0.03320725207788486 0.3172877737402174 chr10 135534747 6814302 0.05027715881596031 0.4260958476277452 chr11 135006516 6303048 0.04668699101901126 0.34186633809736805 chr12 133851895 5627991 0.042046405095721655 0.23389744069874047 chr13 115169878 2163015 0.018781082671633986 0.14980230589683374 chr14 107349540 3939432 0.036697241553154306 0.23027107508048011 chr15 102531392 2014047 0.019643223023832545 0.15695593248734657 chr16 90354753 2706726 0.02995665319344075 0.2136837789878932 chr17 81195210 2208357 0.02719811919939612 0.20983369630532345 chr18 78077248 4285362 0.05488618143918187 0.5758921830356851 chr19 59128983 1882218 0.03183240949704817 0.34007579652496794 chr20 63025520 3240123 0.05140969880137443 0.25439216384959923 chr21 48129895 1499436 0.031153942887263728 0.21206298265158632 chr22 51304566 872654 0.0170092852944122 0.14169553288810222 chrMT 16571 2902 0.17512521875565748 0.44352716799774733 chrX 155270560 4286336 0.027605593745523942 0.2194770050644748 chrY 59373566 233757 0.003937055086096732 0.10097992621433152