BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156421.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 = 3,265,614 number of mapped reads = 3,206,396 (98.19%) number of supplementary alignments = 378,031 (11.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,600,758 number of mapped paired reads (second in pair) = 1,605,638 number of mapped paired reads (both in pair) = 3,169,252 number of mapped paired reads (singletons) = 37,144 number of mapped bases = 367,578,078 bp number of sequenced bases = 367,360,290 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,567,291 duplication rate = 65.86% >>>>>>> Insert size mean insert size = 920,884.8969 std insert size = 8,934,750.6002 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 52.7392 >>>>>>> ACTG content number of A's = 109,721,816 bp (29.87%) number of C's = 73,177,140 bp (19.92%) number of T's = 108,816,590 bp (29.62%) number of G's = 75,642,191 bp (20.59%) number of N's = 2,553 bp (0%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 2,997,903 number of insertions = 38,358 mapped reads with insertion percentage = 1.15% number of deletions = 88,556 mapped reads with deletion percentage = 2.7% homopolymer indels = 42.27% >>>>>>> Coverage mean coverageData = 0.1187X std coverageData = 2.2356X There is a 2.51% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 1.43% of reference with a coverageData >= 3X There is a 1.16% of reference with a coverageData >= 4X There is a 0.87% of reference with a coverageData >= 5X There is a 0.72% of reference with a coverageData >= 6X There is a 0.54% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% 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 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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% 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 27362791 0.10978023200190944 1.1300939377145067 chr2 243199373 35037025 0.14406708606111415 6.913782660927004 chr3 198022430 25419925 0.12836891760191005 1.0896853092282837 chr4 191154276 22151081 0.11588064605993957 1.1978695242584974 chr5 180915260 22353113 0.12355570779380358 1.0713950534885348 chr6 171115067 23843765 0.13934345711356907 1.2687828177638751 chr7 159138663 22499821 0.14138500711169102 1.3663769480671488 chr8 146364022 20065334 0.13709198289180657 1.434493386184572 chr9 141213431 16165498 0.11447564077669072 1.275428382977577 chr10 135534747 17406982 0.1284318773251556 1.5028161886303109 chr11 135006516 15769845 0.11680802873247985 1.0343477649041815 chr12 133851895 17509506 0.13081253724499006 1.122396931822337 chr13 115169878 10789014 0.09367913023229911 0.9339563484328773 chr14 107349540 9598724 0.08941560438917577 0.8964434311882556 chr15 102531392 10639470 0.10376792699742143 0.981642391070668 chr16 90354753 11962335 0.13239297992436547 1.207183491935686 chr17 81195210 10258219 0.12634019913243652 1.109585900469088 chr18 78077248 9790329 0.12539285452274138 1.4723484844926342 chr19 59128983 7008488 0.11852881014374964 1.0867490810517653 chr20 63025520 8172702 0.1296729007551227 1.105097944531012 chr21 48129895 5153977 0.1070847339268037 1.114937455906975 chr22 51304566 4435854 0.08646119333706087 0.9557881388187435 chrMT 16571 289829 17.490133365518073 21.001314902058095 chrX 155270560 11107425 0.0715359370121419 0.8020950186111032 chrY 59373566 2787026 0.04694051895080716 0.7684965505457555