BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714088.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 496,190 number of mapped reads = 326,452 (65.79%) number of supplementary alignments = 11,627 (2.34%) number of secondary alignments = 0 number of mapped bases = 41,658,076 bp number of sequenced bases = 40,854,295 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 258,491 duplication rate = 42.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.5687 >>>>>>> ACTG content number of A's = 11,121,773 bp (27.22%) number of C's = 8,741,509 bp (21.4%) number of T's = 10,555,110 bp (25.84%) number of G's = 10,435,654 bp (25.54%) number of N's = 249 bp (0%) GC percentage = 46.94% >>>>>>> Mismatches and indels general error rate = 0.0424 number of mismatches = 1,587,066 number of insertions = 45,842 mapped reads with insertion percentage = 13.56% number of deletions = 137,386 mapped reads with deletion percentage = 40.15% homopolymer indels = 29.25% >>>>>>> Coverage mean coverageData = 0.0135X std coverageData = 1.9835X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3697837 0.014835818603637502 1.5438470578008436 chr2 243199373 4681799 0.01925086788772272 5.167879928357273 chr3 198022430 2148332 0.010848932618390756 1.0158424767039005 chr4 191154276 1745189 0.009129740838232675 0.974506506506402 chr5 180915260 2239851 0.012380663742793173 1.156300979728654 chr6 171115067 1524866 0.008911348525492498 0.8157320231207013 chr7 159138663 1613922 0.010141608390916292 1.0057094403012836 chr8 146364022 1991903 0.013609239297892484 1.555393207075721 chr9 141213431 1594010 0.01128794894870871 1.231693769111673 chr10 135534747 2272289 0.016765361284069833 1.6414133905570931 chr11 135006516 1933882 0.014324360462720185 1.3939074612305329 chr12 133851895 1779441 0.013294103904916699 1.3675894723477025 chr13 115169878 1070263 0.009292907299945216 0.9382888944634927 chr14 107349540 1340258 0.012484990620360367 1.3013532499744762 chr15 102531392 1251324 0.012204301293402902 1.2188292743575857 chr16 90354753 1498671 0.016586520910526977 1.8806151059773377 chr17 81195210 1531301 0.01885949922415374 1.872844516665382 chr18 78077248 941727 0.012061477884056569 0.9929995513222433 chr19 59128983 923279 0.015614660580243703 1.6148783355839293 chr20 63025520 1119253 0.01775872694108672 1.4508039541312536 chr21 48129895 325360 0.006760039680119809 0.6574916225938111 chr22 51304566 521567 0.010166093208935828 1.1534179008316316 chrMT 16571 427837 25.818417717699596 237.22397431896897 chrX 155270560 3366815 0.0216835374329815 1.3924096838312061 chrY 59373566 117100 0.0019722581594644323 0.26835470991849036