BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085037.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,951,053 number of mapped reads = 2,647,672 (89.72%) number of supplementary alignments = 18,577 (0.63%) number of secondary alignments = 0 number of mapped bases = 175,013,431 bp number of sequenced bases = 174,950,851 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,439 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1409 >>>>>>> ACTG content number of A's = 48,635,267 bp (27.8%) number of C's = 34,220,015 bp (19.56%) number of T's = 52,872,000 bp (30.22%) number of G's = 39,205,083 bp (22.41%) number of N's = 18,486 bp (0.01%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,604,857 number of insertions = 13,227 mapped reads with insertion percentage = 0.5% number of deletions = 36,508 mapped reads with deletion percentage = 1.37% homopolymer indels = 45.19% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.3993X There is a 4.73% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 13746317 0.05515058275421508 0.556810861509097 chr2 243199373 16131499 0.0663303478171385 0.55524287427761 chr3 198022430 11577808 0.05846715445315968 0.2810461525777018 chr4 191154276 10594422 0.055423410983492724 0.28199039436595746 chr5 180915260 8825803 0.04878418216351678 0.2545361354141689 chr6 171115067 11488489 0.06713896795540512 0.4049751215081886 chr7 159138663 14492375 0.0910675930461977 0.5154410555696989 chr8 146364022 9962818 0.06806876351074856 0.5895887792300128 chr9 141213431 5339787 0.037813591541444806 0.348802568645256 chr10 135534747 11796317 0.08703537108458247 0.49210676976221385 chr11 135006516 7477891 0.05538911173739199 0.3782458120736128 chr12 133851895 7739077 0.05781821019418515 0.28377962148365193 chr13 115169878 3621229 0.03144250096366343 0.203927940291887 chr14 107349540 6046230 0.05632283100607604 0.28788017818624884 chr15 102531392 4104650 0.040033105178168264 0.2422056011323144 chr16 90354753 5115463 0.056615317182041325 0.2948986694343492 chr17 81195210 3712362 0.045721440956923445 0.2743487595481629 chr18 78077248 4440721 0.0568759928628632 0.5814239956108402 chr19 59128983 3208096 0.05425589680783111 0.45189826607953937 chr20 63025520 4138829 0.06566909721649263 0.30221705793081766 chr21 48129895 2082687 0.043272211584920346 0.25319620042975005 chr22 51304566 1432080 0.02791330502630117 0.1940437349556176 chrMT 16571 74756 4.511254601412105 3.969825377106143 chrX 155270560 7266405 0.04679834348507534 0.27751943332118284 chrY 59373566 597320 0.010060369289592612 0.14940267976348323