BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525131.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 = 920,715 number of mapped reads = 810,229 (88%) number of supplementary alignments = 21,799 (2.37%) number of secondary alignments = 0 number of mapped bases = 61,690,117 bp number of sequenced bases = 61,664,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,636 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9162 >>>>>>> ACTG content number of A's = 16,279,942 bp (26.4%) number of C's = 12,340,829 bp (20.01%) number of T's = 19,278,790 bp (31.26%) number of G's = 13,762,940 bp (22.32%) number of N's = 2,314 bp (0%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 481,734 number of insertions = 5,316 mapped reads with insertion percentage = 0.65% number of deletions = 14,759 mapped reads with deletion percentage = 1.8% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.0199X std coverageData = 0.2393X There is a 1.83% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 6067664 0.024343626409660982 0.41265311276886607 chr2 243199373 5276947 0.02169802880207261 0.31464997428123787 chr3 198022430 4052200 0.02046333842080415 0.1514565732811017 chr4 191154276 4052456 0.021199923354055652 0.15891287825799746 chr5 180915260 3745663 0.020703963833675502 0.15346693839367595 chr6 171115067 3519875 0.020570222492447145 0.1655743177188703 chr7 159138663 3385522 0.021274038226650176 0.31946116439320726 chr8 146364022 1746247 0.01193084868903097 0.2502836474123605 chr9 141213431 2558972 0.018121307455521 0.2127722182945412 chr10 135534747 2878588 0.021238745515199876 0.2509114152111084 chr11 135006516 3439976 0.025480073865471797 0.29523615304813744 chr12 133851895 2767613 0.020676681491883248 0.1516438057018983 chr13 115169878 2301960 0.019987517916794182 0.1500104600183678 chr14 107349540 1836185 0.01710473095646241 0.15031897717473758 chr15 102531392 1714992 0.016726506551281387 0.13581991661014836 chr16 90354753 1355178 0.014998414084536317 0.13972996993675774 chr17 81195210 1798299 0.022147845913570517 0.17629156713312824 chr18 78077248 1669838 0.021386998681101055 0.36536825036354803 chr19 59128983 1144366 0.019353723706020787 0.3191004110655379 chr20 63025520 1219656 0.019351780040846946 0.15448344888235574 chr21 48129895 791343 0.01644181854126214 0.14063203072833977 chr22 51304566 623284 0.012148704269323709 0.11523266722774 chrMT 16571 5034 0.30378371854444514 0.6803691824436208 chrX 155270560 3596154 0.023160565660354415 0.19919362074470043 chrY 59373566 142105 0.00239340517293504 0.06664895627927685