BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013290.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 = 2,367,782 number of mapped reads = 2,142,715 (90.49%) number of supplementary alignments = 13,629 (0.58%) number of secondary alignments = 0 number of mapped bases = 143,865,160 bp number of sequenced bases = 143,796,735 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,704 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3118 >>>>>>> ACTG content number of A's = 40,650,451 bp (28.27%) number of C's = 26,016,913 bp (18.09%) number of T's = 46,057,107 bp (32.03%) number of G's = 31,070,213 bp (21.61%) number of N's = 2,051 bp (0%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 1,021,291 number of insertions = 10,348 mapped reads with insertion percentage = 0.48% number of deletions = 39,383 mapped reads with deletion percentage = 1.82% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.0465X std coverageData = 0.4813X There is a 3.94% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.08% 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% 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 8468693 0.03397661745444558 0.9087949406148258 chr2 243199373 13517522 0.055582059415917984 0.4268811856476262 chr3 198022430 10936886 0.055230541307871035 0.2657014184761753 chr4 191154276 9766231 0.05109083199373474 0.26832773552643396 chr5 180915260 8277501 0.04575347043693274 0.24500552485200425 chr6 171115067 7192844 0.042035129495639326 0.36196612455425015 chr7 159138663 10563276 0.06637781040048074 1.0556786224457395 chr8 146364022 12546546 0.08572151699958068 0.5613242804675735 chr9 141213431 4730433 0.03349846375448522 0.3480360002328396 chr10 135534747 8102334 0.05978049304212742 0.4406611842857882 chr11 135006516 7272584 0.05386839254484576 0.4066030586672056 chr12 133851895 5291094 0.03952946650475139 0.23354937767112025 chr13 115169878 2325420 0.02019121701249002 0.16061266937321944 chr14 107349540 4737863 0.04413491664705783 0.2548288168100211 chr15 102531392 4118419 0.04016739575719405 0.23403847239311812 chr16 90354753 3465570 0.038355148843138336 0.24849283644022357 chr17 81195210 4233521 0.05214003387638261 0.37864000827909966 chr18 78077248 2594010 0.03322363513632038 0.6881253938089469 chr19 59128983 2791803 0.047215474685231774 0.5608123993509202 chr20 63025520 2936131 0.046586382785893714 0.2508667616922494 chr21 48129895 2778669 0.05773270438258799 0.2895637597482172 chr22 51304566 1332108 0.025964706533137812 0.17929576573861725 chrMT 16571 3234 0.19516021966085328 0.4608144962746672 chrX 155270560 5623024 0.036214360275379956 0.251598397219965 chrY 59373566 259444 0.004369688692776176 0.12479564803639277