BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472702.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,230,318 number of mapped reads = 15,092,324 (99.09%) number of supplementary alignments = 50,924 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,568,083 number of mapped paired reads (second in pair) = 7,524,241 number of mapped paired reads (both in pair) = 15,014,222 number of mapped paired reads (singletons) = 78,102 number of mapped bases = 1,480,663,659 bp number of sequenced bases = 1,480,471,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,246,927 duplication rate = 45.81% >>>>>>> Insert size mean insert size = 23,145.4365 std insert size = 1,513,489.3214 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 55.0458 >>>>>>> ACTG content number of A's = 394,771,417 bp (26.67%) number of C's = 348,124,881 bp (23.51%) number of T's = 392,164,996 bp (26.49%) number of G's = 345,122,267 bp (23.31%) number of N's = 288,028 bp (0.02%) GC percentage = 46.83% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 8,484,667 number of insertions = 86,438 mapped reads with insertion percentage = 0.56% number of deletions = 78,307 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.4783X std coverageData = 16.053X There is a 4.7% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 175377747 0.7036201005091979 24.5756084544089 chr2 243199373 102074270 0.41971436332609297 14.186712547136235 chr3 198022430 166464774 0.8406359521999603 18.4548953504208 chr4 191154276 50089551 0.26203730331410424 10.28116849634916 chr5 180915260 81502093 0.4504987196768255 16.27303142471899 chr6 171115067 96858199 0.5660413235264665 15.069551159168203 chr7 159138663 73759334 0.4634909745345793 15.900669307939262 chr8 146364022 55644236 0.3801770082541186 14.745073145243953 chr9 141213431 70881137 0.5019433101940566 12.61255664219716 chr10 135534747 40803367 0.30105465869944037 10.513076652982804 chr11 135006516 80313621 0.5948869978986792 18.665166244089793 chr12 133851895 72289588 0.5400714573372308 19.179728622291307 chr13 115169878 28419123 0.24675829733882326 9.211983916340042 chr14 107349540 38783521 0.3612826007451918 16.033814519755662 chr15 102531392 33708819 0.3287658378811438 9.581820764240152 chr16 90354753 47125376 0.5215594579733952 14.288027238343757 chr17 81195210 55034913 0.6778098486351596 14.36904702426529 chr18 78077248 21684389 0.27772993484606423 10.309556621152412 chr19 59128983 41754322 0.7061566068200429 20.01074871729188 chr20 63025520 40332127 0.6399332683014753 26.95051796989031 chr21 48129895 6428858 0.13357307345050307 5.006528456512336 chr22 51304566 14363092 0.27995738235072487 9.307098910729021 chrMT 16571 4003 0.24156659223945448 0.6362176674930258 chrX 155270560 82308772 0.530099021991033 18.020748508520384 chrY 59373566 4658427 0.07845961281827 6.033767519699629