BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525102.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 = 638,706 number of mapped reads = 572,153 (89.58%) number of supplementary alignments = 18,027 (2.82%) number of secondary alignments = 0 number of mapped bases = 43,598,724 bp number of sequenced bases = 43,581,271 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,693 duplication rate = 1.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1548 >>>>>>> ACTG content number of A's = 11,588,115 bp (26.59%) number of C's = 8,491,539 bp (19.48%) number of T's = 12,977,127 bp (29.78%) number of G's = 10,522,895 bp (24.15%) number of N's = 1,595 bp (0%) GC percentage = 43.63% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 334,432 number of insertions = 4,198 mapped reads with insertion percentage = 0.72% number of deletions = 10,004 mapped reads with deletion percentage = 1.72% homopolymer indels = 42.13% >>>>>>> Coverage mean coverageData = 0.0141X std coverageData = 0.18X There is a 1.32% of reference with a coverageData >= 1X There is a 0.06% 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 4346359 0.017437705802145223 0.30704771909210327 chr2 243199373 3728339 0.015330380806532753 0.23193454396906682 chr3 198022430 2672149 0.013494173362078225 0.12063862113358448 chr4 191154276 2757352 0.014424746637632109 0.13021902644328087 chr5 180915260 2514262 0.013897456743007748 0.12341705988433803 chr6 171115067 2491682 0.014561441278575428 0.13333505709794444 chr7 159138663 2379320 0.014951237839669422 0.23302204810493252 chr8 146364022 1254187 0.008568956925766907 0.19941729352238252 chr9 141213431 1820410 0.012891195880652457 0.16557488732528447 chr10 135534747 2066337 0.015245809991440793 0.18184880043532378 chr11 135006516 2463885 0.018250119127583442 0.19416728622090362 chr12 133851895 1958298 0.014630334520105225 0.12597783433219595 chr13 115169878 1540520 0.013376066960841966 0.12016478385661795 chr14 107349540 1272004 0.011849179791548245 0.1183381119639326 chr15 102531392 1188111 0.01158777791683546 0.11172980851183223 chr16 90354753 1050957 0.011631452304451543 0.11760240401152475 chr17 81195210 1450385 0.01786293797380412 0.15174638832335519 chr18 78077248 1151312 0.014745806614495429 0.2603730773174869 chr19 59128983 952373 0.016106703543336775 0.21815139085397378 chr20 63025520 908885 0.014420904420939327 0.1256024972972444 chr21 48129895 579202 0.012034142189589236 0.1195307781632401 chr22 51304566 521464 0.010164085590354668 0.10454436621259848 chrMT 16571 461 0.02781968499185324 0.1644559215072759 chrX 155270560 2416536 0.015563388191554148 0.15199562416352136 chrY 59373566 113934 0.0019189347663571361 0.05826382165612536