BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008820.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 = 4,344,817 number of mapped reads = 1,294,928 (29.8%) number of supplementary alignments = 7,029 (0.16%) number of secondary alignments = 0 number of mapped bases = 78,581,269 bp number of sequenced bases = 78,544,230 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,392 duplication rate = 5.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6048 >>>>>>> ACTG content number of A's = 22,766,146 bp (28.99%) number of C's = 13,883,645 bp (17.68%) number of T's = 23,575,514 bp (30.02%) number of G's = 18,299,785 bp (23.3%) number of N's = 19,140 bp (0.02%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 752,673 number of insertions = 5,342 mapped reads with insertion percentage = 0.41% number of deletions = 23,300 mapped reads with deletion percentage = 1.78% homopolymer indels = 47.18% >>>>>>> Coverage mean coverageData = 0.0254X std coverageData = 0.2556X There is a 1.88% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 6816015 0.027346030162949925 0.3659789964740941 chr2 243199373 6807812 0.027992720195047543 0.297281240416752 chr3 198022430 5968530 0.03014067648801199 0.22838616547933244 chr4 191154276 4346138 0.02273628448677758 0.20473284089525115 chr5 180915260 4817812 0.026630213504377685 0.21458955648979208 chr6 171115067 4634140 0.027082010259213467 0.23255132083222532 chr7 159138663 4406878 0.027692063744433996 0.28342146924090406 chr8 146364022 4755879 0.03249349761651125 0.33201108809266183 chr9 141213431 3099616 0.02194986679418617 0.2454898781630219 chr10 135534747 3681573 0.02716331480664512 0.2750465801268894 chr11 135006516 3688040 0.027317496290327203 0.25088667575586165 chr12 133851895 3714387 0.02774997694279935 0.22004024656916166 chr13 115169878 2470605 0.021451833091287984 0.19308370854788842 chr14 107349540 2181882 0.020325024215287743 0.19088973955291078 chr15 102531392 1994690 0.019454432063109022 0.1816109007493433 chr16 90354753 1929343 0.021352977413374146 0.20737935470448027 chr17 81195210 1967191 0.024227919356326563 0.21570753469179027 chr18 78077248 1747881 0.022386560038591526 0.3541041681476511 chr19 59128983 1412760 0.023892851328087276 0.2665943133672935 chr20 63025520 1594107 0.02529304002569118 0.21022901426449933 chr21 48129895 892915 0.01855219089923217 0.1885722214788378 chr22 51304566 819477 0.0159727888546996 0.16382954893225282 chrMT 16571 24407 1.4728742984732364 1.9436569137899136 chrX 155270560 4581648 0.0295075125638756 0.2375383087786282 chrY 59373566 227543 0.003832395716302437 0.10905322627578386