BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714171.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 = 1,729,792 number of mapped reads = 115,333 (6.67%) number of supplementary alignments = 2,398 (0.14%) number of secondary alignments = 0 number of mapped bases = 10,076,627 bp number of sequenced bases = 10,039,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,832 duplication rate = 28.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 19.6552 >>>>>>> ACTG content number of A's = 496,628 bp (4.95%) number of C's = 259,518 bp (2.58%) number of T's = 337,280 bp (3.36%) number of G's = 8,944,655 bp (89.09%) number of N's = 1,636 bp (0.02%) GC percentage = 91.68% >>>>>>> Mismatches and indels general error rate = 0.0305 number of mismatches = 237,842 number of insertions = 10,661 mapped reads with insertion percentage = 6.51% number of deletions = 6,848 mapped reads with deletion percentage = 5.73% homopolymer indels = 55.74% >>>>>>> Coverage mean coverageData = 0.0033X std coverageData = 10.6441X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 66452 2.6660715922549296E-4 0.08297136155527353 chr2 243199373 8853812 0.03640557083179651 37.97046469306591 chr3 198022430 66176 3.341843648722016E-4 0.10526297699126538 chr4 191154276 36074 1.8871667824998066E-4 0.06503116164675087 chr5 180915260 42028 2.3230765608163732E-4 0.068441952875415 chr6 171115067 67557 3.948045089448494E-4 0.1621493124995047 chr7 159138663 69109 4.3426907513983575E-4 0.44392622029794654 chr8 146364022 53200 3.6347730318588814E-4 0.1186742208782423 chr9 141213431 29687 2.1022787839493823E-4 0.07615084634645164 chr10 135534747 42846 3.161255762701206E-4 0.09014184487820197 chr11 135006516 50566 3.7454488492985036E-4 0.14350651807886386 chr12 133851895 56229 4.200837052026794E-4 0.16587215653690568 chr13 115169878 33776 2.9327112771622454E-4 0.16500200696689019 chr14 107349540 59339 5.527643621015982E-4 0.33348983415779093 chr15 102531392 12413 1.2106536113349558E-4 0.029440693380400063 chr16 90354753 14775 1.6352211155953246E-4 0.04654258732727817 chr17 81195210 35541 4.3772286567150945E-4 0.18801697268553588 chr18 78077248 16234 2.0792228742488465E-4 0.0640574386784299 chr19 59128983 17560 2.969778796973389E-4 0.10001014445049675 chr20 63025520 45114 7.158052801468358E-4 0.34666709981851895 chr21 48129895 17607 3.658225308823134E-4 0.1052060504317249 chr22 51304566 3009 5.864975058945046E-5 0.012039701754760912 chrMT 16571 12117 0.7312171866513789 6.42921553785967 chrX 155270560 370186 0.0023841351509262284 0.33096182796312873 chrY 59373566 5220 8.791791283009681E-5 0.029626105895648732