BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472658.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 = 16,013,266 number of mapped reads = 15,879,757 (99.17%) number of supplementary alignments = 91,027 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,974,261 number of mapped paired reads (second in pair) = 7,905,496 number of mapped paired reads (both in pair) = 15,782,390 number of mapped paired reads (singletons) = 97,367 number of mapped bases = 1,566,122,804 bp number of sequenced bases = 1,565,924,069 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,986,992 duplication rate = 48.44% >>>>>>> Insert size mean insert size = 23,308.3787 std insert size = 1,484,883.6786 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 54.7069 >>>>>>> ACTG content number of A's = 422,288,436 bp (26.97%) number of C's = 361,985,057 bp (23.12%) number of T's = 425,283,654 bp (27.16%) number of G's = 356,072,035 bp (22.74%) number of N's = 294,887 bp (0.02%) GC percentage = 45.86% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 9,297,588 number of insertions = 97,266 mapped reads with insertion percentage = 0.61% number of deletions = 83,125 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.52% >>>>>>> Coverage mean coverageData = 0.5059X std coverageData = 24.4634X There is a 3.12% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 199278510 0.799510585773024 38.569817338588535 chr2 243199373 128320037 0.52763309138959 22.477920150215763 chr3 198022430 132499338 0.6691127767697831 21.314153583534765 chr4 191154276 52582137 0.2750769593038034 22.277045798726526 chr5 180915260 55955585 0.30929168164144916 13.080568330298725 chr6 171115067 94616948 0.5529434062051356 19.805130162883867 chr7 159138663 114871164 0.7218306465223979 41.78240027095589 chr8 146364022 59657008 0.40759339067629613 12.6520401638197 chr9 141213431 101270319 0.7171436759439688 29.094292572556967 chr10 135534747 31235808 0.23046346926814273 11.122149984654637 chr11 135006516 27706668 0.2052246722669297 7.944196959194073 chr12 133851895 112230418 0.8384671580480799 37.25915990972415 chr13 115169878 60461384 0.5249756711559597 27.77473900263559 chr14 107349540 27548860 0.25662764833458995 12.358226260670351 chr15 102531392 12069686 0.11771698174155287 5.0572838505005935 chr16 90354753 94509774 1.0459856384090829 42.10362393111083 chr17 81195210 54098059 0.6662715571522014 20.46357061071331 chr18 78077248 8476166 0.10856128023364758 4.587856469592805 chr19 59128983 33963508 0.5743969585947386 20.62506487400935 chr20 63025520 70139239 1.112870453111692 33.515334536564254 chr21 48129895 9802173 0.203660801670147 12.350107590201509 chr22 51304566 16886953 0.32915107399992427 14.24510994586072 chrMT 16571 5505 0.332206867418985 0.7012235827438399 chrX 155270560 63573653 0.4094379063230016 11.32738707798382 chrY 59373566 4363904 0.07349910564576835 10.609404515821105