BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716182.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 = 2,154,314 number of mapped reads = 1,903,686 (88.37%) number of supplementary alignments = 7,236 (0.34%) number of secondary alignments = 0 number of mapped bases = 108,511,471 bp number of sequenced bases = 108,479,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,448 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0789 >>>>>>> ACTG content number of A's = 26,572,748 bp (24.5%) number of C's = 20,533,847 bp (18.93%) number of T's = 34,592,723 bp (31.89%) number of G's = 26,779,141 bp (24.69%) number of N's = 897 bp (0%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 567,734 number of insertions = 8,823 mapped reads with insertion percentage = 0.46% number of deletions = 19,927 mapped reads with deletion percentage = 1.04% homopolymer indels = 39.67% >>>>>>> Coverage mean coverageData = 0.0351X std coverageData = 0.275X There is a 3.12% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 9141580 0.0366762576691835 0.32665498177463675 chr2 243199373 8464251 0.03480375337974247 0.41173108036792744 chr3 198022430 6176267 0.031189734415439707 0.19717690596595536 chr4 191154276 6600638 0.03453042295533059 0.23212728951031075 chr5 180915260 6118101 0.033817495550126614 0.20186208310350623 chr6 171115067 5742181 0.033557424840911294 0.24107669633635267 chr7 159138663 6099381 0.03832746163011311 0.3856138613168642 chr8 146364022 5568439 0.038045135163066235 0.25421928004188876 chr9 141213431 3613433 0.025588451285487143 0.20785965456173244 chr10 135534747 4831535 0.03564794347533626 0.3622159312858277 chr11 135006516 3859663 0.028588716414250703 0.2346237941509228 chr12 133851895 5433663 0.040594591507277504 0.22173867448322848 chr13 115169878 3248275 0.028204206311653816 0.18501713458595048 chr14 107349540 3640398 0.0339116311071291 0.21276150709061292 chr15 102531392 4013246 0.0391416318623666 0.2231387505435455 chr16 90354753 3869199 0.042822307311271166 0.24932491992290173 chr17 81195210 4965679 0.06115728994358165 0.2906547682065365 chr18 78077248 2010072 0.025744657393662235 0.33135147127954157 chr19 59128983 2976813 0.05034439709541427 0.3365332649664481 chr20 63025520 3571580 0.05666879067399999 0.2823033245603706 chr21 48129895 1355761 0.028168791974302044 0.20299690100444875 chr22 51304566 1031509 0.020105598398395964 0.1565068412778006 chrMT 16571 10325 0.6230764588739364 1.1014480613640403 chrX 155270560 5835517 0.037582894014164696 0.23042484904169902 chrY 59373566 333965 0.005624809532242008 0.1607204161997113