BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238671.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,989,002 number of mapped reads = 2,010,750 (67.27%) number of supplementary alignments = 18,042 (0.6%) number of secondary alignments = 0 number of mapped bases = 119,599,708 bp number of sequenced bases = 119,546,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,079,779 duplication rate = 21.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5072 >>>>>>> ACTG content number of A's = 29,584,648 bp (24.75%) number of C's = 20,422,438 bp (17.08%) number of T's = 41,053,382 bp (34.34%) number of G's = 28,481,024 bp (23.82%) number of N's = 5,311 bp (0%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 747,976 number of insertions = 7,353 mapped reads with insertion percentage = 0.36% number of deletions = 31,483 mapped reads with deletion percentage = 1.55% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 1.1886X There is a 0.74% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% 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 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% 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 0.03% 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 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% 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 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 8638779 0.034659006927810224 0.8880893690704981 chr2 243199373 6385454 0.026256046309790445 1.5503481438390776 chr3 198022430 12156605 0.061390040512077346 1.1749323376347853 chr4 191154276 7230209 0.037823945931505086 0.8869102403994086 chr5 180915260 5107866 0.028233472400282872 0.7822956559071456 chr6 171115067 10451901 0.06108112618744438 1.5675988389477207 chr7 159138663 5763964 0.03621975886526079 1.125299541910729 chr8 146364022 4720501 0.032251785209892636 1.059022894395258 chr9 141213431 4928697 0.03490246618255455 0.8591555581643898 chr10 135534747 3250997 0.02398644681131105 0.8205534587366123 chr11 135006516 9210698 0.0682240996427165 1.2039336803575231 chr12 133851895 3322306 0.02482076178301398 0.7277623719988343 chr13 115169878 2997296 0.0260249993492222 1.0505570871748604 chr14 107349540 2776666 0.02586565345319598 1.0393684567928532 chr15 102531392 3251376 0.031711029535227614 0.9844620653556809 chr16 90354753 1739279 0.019249446678250563 0.605947507893451 chr17 81195210 3727066 0.045902535383552795 0.9626334321225708 chr18 78077248 13000316 0.1665058174181549 3.7750966416806437 chr19 59128983 1450084 0.024524081532063556 0.7696964939985693 chr20 63025520 1967934 0.03122439925922071 0.792978225398653 chr21 48129895 1170634 0.02432238840329903 0.6799024215297613 chr22 51304566 859536 0.01675359655123094 0.5406045294613187 chrMT 16571 96637 5.831693923118701 12.470297237116295 chrX 155270560 5035690 0.03243171145901708 0.8671102394264415 chrY 59373566 359217 0.006050116646185611 0.45529404841930654