BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251059.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 1,800,008 number of mapped reads = 1,467,591 (81.53%) number of supplementary alignments = 41,131 (2.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 735,138 number of mapped paired reads (second in pair) = 732,453 number of mapped paired reads (both in pair) = 1,457,812 number of mapped paired reads (singletons) = 9,779 number of mapped bases = 178,276,430 bp number of sequenced bases = 178,119,286 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 243,013 duplication rate = 14.86% >>>>>>> Insert size mean insert size = 99,229.9119 std insert size = 3,027,014.5871 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 52.8788 >>>>>>> ACTG content number of A's = 52,246,741 bp (29.33%) number of C's = 36,276,151 bp (20.37%) number of T's = 52,243,790 bp (29.33%) number of G's = 37,347,145 bp (20.97%) number of N's = 5,459 bp (0%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,287,465 number of insertions = 30,811 mapped reads with insertion percentage = 1.96% number of deletions = 74,287 mapped reads with deletion percentage = 4.85% homopolymer indels = 43.03% >>>>>>> Coverage mean coverageData = 0.0576X std coverageData = 0.7276X There is a 3.5% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 15157910 0.060813930730387225 1.5339876823384286 chr2 243199373 15798553 0.0649613229060422 1.0752421105754963 chr3 198022430 12315252 0.06219119722952597 0.3616005573965664 chr4 191154276 10743349 0.05620250420137084 0.4307166464380255 chr5 180915260 10726802 0.05929185851983962 0.36408382909855097 chr6 171115067 10105577 0.05905720154964495 0.4070253773471859 chr7 159138663 9488460 0.05962385143326233 0.9559257412026203 chr8 146364022 8603127 0.058778973701610907 0.4267262471562057 chr9 141213431 7838585 0.05550877805667083 0.8872117864423495 chr10 135534747 10524972 0.07765515657767082 0.8356434521778073 chr11 135006516 8147492 0.06034887975332983 0.44977861685378845 chr12 133851895 7856420 0.05869487316559844 0.36039041085745877 chr13 115169878 5133589 0.044574059547063165 0.31148228068063044 chr14 107349540 5200246 0.04844218242574677 0.34308893271267343 chr15 102531392 5407954 0.052744373157442355 0.33337196301614913 chr16 90354753 5130477 0.05678148442285045 0.6822484743479174 chr17 81195210 5088258 0.06266697259604354 0.42818085349926815 chr18 78077248 4472880 0.05728787981871492 0.7814676925654097 chr19 59128983 3561619 0.06023474139577202 0.788980913756427 chr20 63025520 3702040 0.05873874582867385 0.3665472087488539 chr21 48129895 2126942 0.044191702475145644 0.3284408061667244 chr22 51304566 2215517 0.04318362229201978 0.3157952079535027 chrMT 16571 234167 14.131132701707802 8.139791390101779 chrX 155270560 8291770 0.053402074417713184 0.3548760875838555 chrY 59373566 404472 0.006812324528393663 0.5085244190703455