BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236108.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 = 1,911,395 number of mapped reads = 1,736,765 (90.86%) number of supplementary alignments = 11,778 (0.62%) number of secondary alignments = 0 number of mapped bases = 118,158,532 bp number of sequenced bases = 118,099,224 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,417 duplication rate = 3.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5361 >>>>>>> ACTG content number of A's = 33,565,348 bp (28.42%) number of C's = 21,509,464 bp (18.21%) number of T's = 37,657,734 bp (31.89%) number of G's = 25,308,402 bp (21.43%) number of N's = 58,276 bp (0.05%) GC percentage = 39.64% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 953,189 number of insertions = 9,226 mapped reads with insertion percentage = 0.53% number of deletions = 33,478 mapped reads with deletion percentage = 1.9% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.3935X There is a 3.08% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.1% 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 9398822 0.0377083192904061 0.643274639045921 chr2 243199373 8461064 0.034790648905168024 0.40917161338978064 chr3 198022430 11493498 0.058041394603631516 0.28430622786305304 chr4 191154276 4915947 0.025717169936601367 0.24065759918017682 chr5 180915260 7133701 0.03943117346762236 0.239214929035103 chr6 171115067 12052175 0.0704331606286897 0.4263852590551276 chr7 159138663 7658529 0.04812487962149085 0.5367180738650136 chr8 146364022 7167368 0.048969466007158506 0.7107840993947869 chr9 141213431 5272564 0.037337553252990506 0.39614474776060343 chr10 135534747 4060728 0.029960789317000754 0.3492668846951665 chr11 135006516 4712845 0.03490827805674209 0.2613166987283897 chr12 133851895 1947584 0.014550290827036853 0.1595621484071137 chr13 115169878 5125195 0.04450117590642928 0.2508253764535642 chr14 107349540 2834971 0.026408785729310064 0.21969662673096013 chr15 102531392 3701127 0.03609750075372038 0.22560398683791655 chr16 90354753 3466192 0.038362032819679114 0.2648664814252973 chr17 81195210 3439358 0.04235912438677109 0.29336754590457687 chr18 78077248 4399755 0.05635130736165291 0.6462943465949432 chr19 59128983 1177815 0.019919419212740392 0.4320484042133831 chr20 63025520 1597327 0.025344130441129244 0.19983606558182407 chr21 48129895 1907455 0.0396313974921408 0.27635058904588056 chr22 51304566 490998 0.009570259302066798 0.11123389415508617 chrMT 16571 175017 10.561643835616438 6.527210155293552 chrX 155270560 5282529 0.03402144617756257 0.24719736343087106 chrY 59373566 285968 0.0048164194820301005 0.17599065409166395