BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716369.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 7,009,460 number of mapped reads = 6,334,171 (90.37%) number of supplementary alignments = 143,649 (2.05%) number of secondary alignments = 0 number of mapped bases = 489,053,547 bp number of sequenced bases = 488,843,968 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 567,260 duplication rate = 6.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7902 >>>>>>> ACTG content number of A's = 128,578,654 bp (26.3%) number of C's = 94,004,021 bp (19.23%) number of T's = 151,753,808 bp (31.04%) number of G's = 114,473,587 bp (23.42%) number of N's = 33,898 bp (0.01%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 3,369,343 number of insertions = 42,458 mapped reads with insertion percentage = 0.66% number of deletions = 109,444 mapped reads with deletion percentage = 1.7% homopolymer indels = 42.47% >>>>>>> Coverage mean coverageData = 0.158X std coverageData = 1.2994X There is a 10.74% of reference with a coverageData >= 1X There is a 2.96% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 47543348 0.19074515364998829 2.9140433027344272 chr2 243199373 39678002 0.1631500998976671 1.4177743226364077 chr3 198022430 32878453 0.1660339841299796 0.5544767405433563 chr4 191154276 31154879 0.1629829039241581 0.8265541236098671 chr5 180915260 28259727 0.15620421958877323 0.5484753815885538 chr6 171115067 27484440 0.16061963731107326 0.6575178097003738 chr7 159138663 25671895 0.1613177748012122 1.6122672776935536 chr8 146364022 24019268 0.16410636761539663 1.5126098082540609 chr9 141213431 19557905 0.13849890100042964 1.0234004451008267 chr10 135534747 22792021 0.16816367392488657 1.275644765103806 chr11 135006516 26990362 0.19991895798570197 1.3783184715062502 chr12 133851895 20933103 0.1563900384077491 0.5464809495113587 chr13 115169878 17185908 0.1492222471573687 0.5380868871082437 chr14 107349540 14064762 0.13101837231906163 0.5867443768262233 chr15 102531392 13119113 0.12795215927625367 0.49416485989375525 chr16 90354753 11410491 0.12628545395946134 0.6040796696723654 chr17 81195210 14503347 0.17862318479131958 0.8259757394722295 chr18 78077248 12703019 0.1626980884367236 1.8435557707339625 chr19 59128983 8836360 0.1494421103099304 2.068815456676482 chr20 63025520 9810290 0.15565583592170282 0.6211541927721743 chr21 48129895 6629619 0.1377443063193884 0.6795677119377215 chr22 51304566 5314304 0.10358345103240908 0.443093438131785 chrMT 16571 171826 10.369078510651137 7.309617828710411 chrX 155270560 26867147 0.17303439235357945 0.7746609043889727 chrY 59373566 1473958 0.024825155356173148 0.7269975264078439