BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234027.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 = 7,626,735 number of mapped reads = 4,249,010 (55.71%) number of supplementary alignments = 27,725 (0.36%) number of secondary alignments = 0 number of mapped bases = 286,989,830 bp number of sequenced bases = 286,850,234 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 547,375 duplication rate = 9.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1368 >>>>>>> ACTG content number of A's = 81,446,890 bp (28.39%) number of C's = 51,890,520 bp (18.09%) number of T's = 92,770,092 bp (32.34%) number of G's = 60,671,172 bp (21.15%) number of N's = 71,560 bp (0.02%) GC percentage = 39.24% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 2,315,747 number of insertions = 25,912 mapped reads with insertion percentage = 0.6% number of deletions = 78,044 mapped reads with deletion percentage = 1.81% homopolymer indels = 45.48% >>>>>>> Coverage mean coverageData = 0.0927X std coverageData = 1.1229X There is a 4.39% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 8040566 0.03225896075099448 0.5130989539946728 chr2 243199373 4219202 0.01734873716142352 0.8553682564613878 chr3 198022430 25148422 0.1269978456480915 0.6784811277559888 chr4 191154276 5446984 0.028495224454199497 0.46111483508698076 chr5 180915260 14535141 0.08034226079104659 0.5477336741788182 chr6 171115067 32525993 0.1900825775909026 1.026460520163161 chr7 159138663 51836806 0.32573357738967557 3.3183276932815593 chr8 146364022 29707303 0.20296861615349707 1.655692987271436 chr9 141213431 11767172 0.08332898589511645 1.003148596871234 chr10 135534747 11053919 0.08155782369225215 0.9078812290691931 chr11 135006516 12958377 0.09598334498166 0.9022829334512816 chr12 133851895 8384673 0.06264142169970773 0.48399523804060185 chr13 115169878 8060979 0.06999207726867611 0.5141571654576832 chr14 107349540 10395047 0.0968336426965593 0.6249817228704282 chr15 102531392 11733200 0.11443519658837754 0.643024232118997 chr16 90354753 2865021 0.03170858095312374 0.5414378775717426 chr17 81195210 6683288 0.08231135802222816 0.6188291131331081 chr18 78077248 1775231 0.022736854147318308 2.296999865115365 chr19 59128983 1119094 0.018926319094647714 0.4547792968530587 chr20 63025520 6655208 0.10559544768531859 0.6196933185628416 chr21 48129895 4604273 0.0956634748527916 0.6560193843600077 chr22 51304566 5564571 0.10846151588145196 0.6351811663608868 chrMT 16571 55646 3.3580351215979722 3.5364983060898463 chrX 155270560 10973699 0.07067469196993945 0.5964070785260313 chrY 59373566 880015 0.014821663229727519 0.41043937564278793