BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013171.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,260,917 number of mapped reads = 2,027,816 (89.69%) number of supplementary alignments = 17,075 (0.76%) number of secondary alignments = 0 number of mapped bases = 135,841,203 bp number of sequenced bases = 135,782,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,826 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2285 >>>>>>> ACTG content number of A's = 38,144,033 bp (28.09%) number of C's = 24,884,609 bp (18.33%) number of T's = 43,354,187 bp (31.93%) number of G's = 29,398,385 bp (21.65%) number of N's = 1,784 bp (0%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 952,970 number of insertions = 9,927 mapped reads with insertion percentage = 0.49% number of deletions = 33,826 mapped reads with deletion percentage = 1.65% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.0439X std coverageData = 0.3586X There is a 3.47% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 1806715 0.007248587757781354 0.33466535754895044 chr2 243199373 20299884 0.08347013295959443 0.4755283249577835 chr3 198022430 2123310 0.010722573195369837 0.12333814644761366 chr4 191154276 9442666 0.049398141635084325 0.27753175967926097 chr5 180915260 11074233 0.06121226589730463 0.30443253176873775 chr6 171115067 8009555 0.04680800551596079 0.39018765053948345 chr7 159138663 6493898 0.04080653863480052 0.521300130646954 chr8 146364022 7945823 0.05428808863970683 0.5113779697315364 chr9 141213431 8730101 0.061822030228838504 0.4082356630441794 chr10 135534747 3955140 0.029181741859893685 0.33232311118831404 chr11 135006516 3121134 0.02311839526323307 0.2551036759947957 chr12 133851895 10752463 0.08033104798404236 0.3490553555674788 chr13 115169878 4323175 0.03753737587531351 0.23366697057417649 chr14 107349540 4464653 0.041589866151266225 0.28091644397991583 chr15 102531392 5117570 0.04991222590638387 0.27207921442567257 chr16 90354753 2828538 0.031304805846793696 0.24791011928710258 chr17 81195210 4410433 0.05431888161875559 0.30895811916815497 chr18 78077248 4857799 0.06221785634657615 0.709123760267571 chr19 59128983 3046660 0.05152566212748831 0.35434134216142776 chr20 63025520 1288860 0.02044981144146054 0.17816526366658847 chr21 48129895 1249644 0.02596398766296914 0.21632697676528984 chr22 51304566 893897 0.01742334200819475 0.15514671345639416 chrMT 16571 105686 6.377768390561825 4.8568088992770875 chrX 155270560 9224438 0.05940880228679538 0.3449358940981587 chrY 59373566 274928 0.004630478149148057 0.10451697466685846