BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524657.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 = 2,287,810 number of mapped reads = 2,124,718 (92.87%) number of supplementary alignments = 9,615 (0.42%) number of secondary alignments = 0 number of mapped bases = 126,091,873 bp number of sequenced bases = 126,054,682 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,710 duplication rate = 3.51% >>>>>>> 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 = 31,799,607 bp (25.23%) number of C's = 25,856,398 bp (20.51%) number of T's = 38,069,326 bp (30.2%) number of G's = 30,312,070 bp (24.05%) number of N's = 17,281 bp (0.01%) GC percentage = 44.56% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 627,671 number of insertions = 9,312 mapped reads with insertion percentage = 0.44% number of deletions = 23,449 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.23% >>>>>>> Coverage mean coverageData = 0.0407X std coverageData = 0.3591X There is a 3.57% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% 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 10276002 0.04122758835573774 0.6379439195311014 chr2 243199373 10595006 0.043565104092599775 0.5046789079126554 chr3 198022430 8337637 0.04210450806002128 0.22756895223620607 chr4 191154276 8092133 0.04233299494697152 0.26147794632819155 chr5 180915260 7570483 0.04184546400342348 0.2295386696196186 chr6 171115067 7226903 0.04223417099792855 0.26303336067830657 chr7 159138663 6923390 0.043505392526767675 0.4313409259484071 chr8 146364022 6418331 0.04385183539162377 0.38658108409397807 chr9 141213431 5333636 0.037770033361769956 0.30507711925774034 chr10 135534747 6114970 0.045117360199890294 0.36512253864776767 chr11 135006516 5758769 0.042655489309864125 0.31846244754958813 chr12 133851895 5684849 0.0424711880246447 0.2331208375343666 chr13 115169878 3918433 0.0340230715534838 0.20700451921341662 chr14 107349540 3728227 0.03472979017888665 0.2224400678263777 chr15 102531392 3657666 0.035673620816539776 0.21086976142765382 chr16 90354753 3656006 0.04046279668320271 0.2443108705663922 chr17 81195210 3504059 0.04315598173833161 0.2546073868806455 chr18 78077248 3341267 0.04279437461730209 0.5691933799367015 chr19 59128983 2640436 0.0446555287446767 0.49072381234051715 chr20 63025520 2745104 0.043555435956736256 0.23926521692192543 chr21 48129895 1654576 0.03437730333714628 0.24244930649275467 chr22 51304566 1518526 0.029598262267728763 0.19212286840724904 chrMT 16571 2593 0.15647818478064088 0.5640044537846758 chrX 155270560 6992763 0.045035987504649946 0.2635013901102538 chrY 59373566 400108 0.0067388238058667385 0.23615137513535148