BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046546.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 7,996,024 number of mapped reads = 7,967,630 (99.64%) number of supplementary alignments = 38,265 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,987,625 number of mapped paired reads (second in pair) = 3,980,005 number of mapped paired reads (both in pair) = 7,948,080 number of mapped paired reads (singletons) = 19,550 number of mapped bases = 776,527,738 bp number of sequenced bases = 776,320,612 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,873,985 duplication rate = 37.69% >>>>>>> Insert size mean insert size = 19,102.1831 std insert size = 1,441,819.9112 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 52.4054 >>>>>>> ACTG content number of A's = 230,715,648 bp (29.72%) number of C's = 157,699,275 bp (20.31%) number of T's = 231,757,438 bp (29.85%) number of G's = 156,082,080 bp (20.11%) number of N's = 66,171 bp (0.01%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 2,868,376 number of insertions = 65,200 mapped reads with insertion percentage = 0.8% number of deletions = 76,861 mapped reads with deletion percentage = 0.93% homopolymer indels = 49.45% >>>>>>> Coverage mean coverageData = 0.2508X std coverageData = 22.4878X There is a 2.51% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 166905492 0.6696291922177398 49.20529977930507 chr2 243199373 28008324 0.1151661028336615 7.381961894407132 chr3 198022430 60877480 0.3074271939799951 19.780501919104882 chr4 191154276 17564913 0.09188867425597114 4.293325597908978 chr5 180915260 81963240 0.4530476865246193 26.498668033293534 chr6 171115067 39097668 0.22848758256921933 24.554465351315645 chr7 159138663 49007757 0.3079563198290789 19.78850255186299 chr8 146364022 76016486 0.5193659272358613 30.190059398438663 chr9 141213431 8716829 0.06172804483448887 3.299025108126133 chr10 135534747 43413400 0.3203119566084408 32.42615632386095 chr11 135006516 42920634 0.31791527751149434 20.69342730109939 chr12 133851895 7681832 0.05739053600996833 2.8162168974975654 chr13 115169878 14873907 0.1291475449856776 8.194620744261975 chr14 107349540 41052378 0.382417828711702 26.651227291583318 chr15 102531392 8689614 0.08475076589226449 2.986949138901029 chr16 90354753 14920790 0.16513564040178386 12.339370664687927 chr17 81195210 44236111 0.5448118306486306 37.7403984864884 chr18 78077248 4125413 0.05283758208281111 2.8337259994817114 chr19 59128983 2502870 0.04232898779943501 2.1556932617317743 chr20 63025520 11651572 0.1848706999958112 15.438724492174888 chr21 48129895 4619929 0.09598876124703784 11.786760668188329 chr22 51304566 3012308 0.058714228281358034 4.428831639113975 chrMT 16571 38284 2.3103011284774606 2.189424821973869 chrX 155270560 4520063 0.029110882320512014 2.374305539448105 chrY 59373566 110444 0.0018601543993500408 0.15010066647863426