BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174014.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,859,012 number of mapped reads = 6,668,420 (97.22%) number of supplementary alignments = 627,291 (9.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,336,681 number of mapped paired reads (second in pair) = 3,331,739 number of mapped paired reads (both in pair) = 6,545,680 number of mapped paired reads (singletons) = 122,740 number of mapped bases = 788,352,288 bp number of sequenced bases = 787,951,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,167,466 duplication rate = 65.28% >>>>>>> Insert size mean insert size = 667,385.158 std insert size = 7,537,993.4578 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.7886 >>>>>>> ACTG content number of A's = 238,121,540 bp (30.22%) number of C's = 154,050,317 bp (19.55%) number of T's = 237,132,493 bp (30.09%) number of G's = 158,637,513 bp (20.13%) number of N's = 9,187 bp (0%) GC percentage = 39.68% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 7,940,667 number of insertions = 79,245 mapped reads with insertion percentage = 1.15% number of deletions = 154,203 mapped reads with deletion percentage = 2.25% homopolymer indels = 43.89% >>>>>>> Coverage mean coverageData = 0.2547X std coverageData = 3.6602X There is a 5.18% of reference with a coverageData >= 1X There is a 4.13% of reference with a coverageData >= 2X There is a 3.21% of reference with a coverageData >= 3X There is a 2.65% of reference with a coverageData >= 4X There is a 2.03% of reference with a coverageData >= 5X There is a 1.65% of reference with a coverageData >= 6X There is a 1.24% of reference with a coverageData >= 7X There is a 1.01% of reference with a coverageData >= 8X There is a 0.75% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 70391399 0.2824121308809096 1.8654151963044434 chr2 243199373 58579242 0.24086921474094425 10.769651488313523 chr3 198022430 47846931 0.24162379483980678 1.419643779167692 chr4 191154276 48384202 0.25311598051826995 1.8248628028216831 chr5 180915260 38990075 0.21551567844525663 1.3289393171710493 chr6 171115067 39357128 0.23000387218970028 1.471092726685981 chr7 159138663 70895549 0.4454954419216152 4.252627887364421 chr8 146364022 77785233 0.5314505022279314 2.7534319485308774 chr9 141213431 26895229 0.19045800962091206 1.6362029854551572 chr10 135534747 36389108 0.26848545340184976 4.722535264784649 chr11 135006516 32487063 0.24063329654399793 1.4590616431262298 chr12 133851895 30511961 0.227953149262474 1.3850922905274026 chr13 115169878 20419573 0.17729959738257256 1.2098758674140462 chr14 107349540 26069939 0.24285096144799503 1.4367506758464994 chr15 102531392 19616459 0.19132149303112944 1.2532242590206688 chr16 90354753 18202635 0.201457415306088 1.837422606639328 chr17 81195210 19707712 0.24272013090427377 1.57854444272535 chr18 78077248 13458106 0.1723691132146461 2.170697191672177 chr19 59128983 10013250 0.1693458857562289 1.5479190386718171 chr20 63025520 30953518 0.49112673723279077 2.0498110378965753 chr21 48129895 9727615 0.20211170209284687 1.397174059165108 chr22 51304566 8268475 0.16116450531907822 1.1179410304317334 chrMT 16571 2060842 124.36437149236619 97.89738920195606 chrX 155270560 29977381 0.19306545297447242 1.2662540293635063 chrY 59373566 1363663 0.022967510491116536 0.9844378806816553