BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716371.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 = 3,072,502 number of mapped reads = 2,802,455 (91.21%) number of supplementary alignments = 51,726 (1.68%) number of secondary alignments = 0 number of mapped bases = 221,375,390 bp number of sequenced bases = 221,274,744 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 172,443 duplication rate = 4.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5148 >>>>>>> ACTG content number of A's = 56,331,206 bp (25.46%) number of C's = 45,357,513 bp (20.5%) number of T's = 68,419,042 bp (30.92%) number of G's = 51,151,893 bp (23.12%) number of N's = 15,090 bp (0.01%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,526,913 number of insertions = 18,770 mapped reads with insertion percentage = 0.66% number of deletions = 52,195 mapped reads with deletion percentage = 1.83% homopolymer indels = 43.18% >>>>>>> Coverage mean coverageData = 0.0715X std coverageData = 0.5828X There is a 5.68% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18846212 0.07561149466504238 1.0561793562742932 chr2 243199373 10969447 0.04510475033173708 0.6566083587331387 chr3 198022430 15423936 0.0778898430849475 0.3333858691410022 chr4 191154276 15273658 0.07990225654172654 0.47519632557071073 chr5 180915260 14118252 0.07803792781217019 0.3400943039395464 chr6 171115067 13451568 0.0786112423402201 0.38650383652075726 chr7 159138663 12921187 0.08119451776467419 0.8211843837491754 chr8 146364022 6526886 0.04459351356168663 0.7076748586911792 chr9 141213431 9871238 0.06990296836566488 0.5431815609991621 chr10 135534747 11323064 0.08354362442569802 0.6542738189421934 chr11 135006516 10738739 0.07954237556948733 0.5644166616823233 chr12 133851895 10671647 0.07972727618088635 0.3450940270799108 chr13 115169878 7248929 0.06294118849374834 0.29983466938605624 chr14 107349540 7208812 0.06715270507912749 0.3516364825509404 chr15 102531392 6980616 0.06808271948556009 0.31784241939358254 chr16 90354753 6914682 0.07652814899510599 0.37362878341382 chr17 81195210 6607002 0.08137181984011126 0.4180982371320388 chr18 78077248 6241687 0.07994245647592498 0.9190043537675425 chr19 59128983 4851910 0.0820563749591296 0.7202339631092958 chr20 63025520 5272260 0.08365278065139328 0.37427395721576046 chr21 48129895 3203059 0.06655030101353847 0.3913428334581778 chr22 51304566 2864524 0.055833704937685275 0.2961304051944606 chrMT 16571 7108 0.4289421278136504 0.6818709422700335 chrX 155270560 13119332 0.08449336435702944 0.42786047860358967 chrY 59373566 719635 0.012120461149326958 0.41639257394127277