BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716260.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 = 455,090 number of mapped reads = 411,760 (90.48%) number of supplementary alignments = 2,297 (0.5%) number of secondary alignments = 0 number of mapped bases = 24,321,627 bp number of sequenced bases = 24,314,946 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,558 duplication rate = 1.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8918 >>>>>>> ACTG content number of A's = 6,445,944 bp (26.51%) number of C's = 4,977,502 bp (20.47%) number of T's = 7,346,188 bp (30.21%) number of G's = 5,544,968 bp (22.8%) number of N's = 344 bp (0%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 119,068 number of insertions = 1,862 mapped reads with insertion percentage = 0.45% number of deletions = 4,285 mapped reads with deletion percentage = 1.03% homopolymer indels = 39.08% >>>>>>> Coverage mean coverageData = 0.0079X std coverageData = 0.1097X There is a 0.75% of reference with a coverageData >= 1X There is a 0.02% 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 1998267 0.00801709938367616 0.14251732733337352 chr2 243199373 2392562 0.009837862534291978 0.11970221128172487 chr3 198022430 1843880 0.009311470422820283 0.10051517950474134 chr4 191154276 1351809 0.007071821924611302 0.08948036936419514 chr5 180915260 1216456 0.006723899354869236 0.08426279650579804 chr6 171115067 1336317 0.007809464259509071 0.09310649434957846 chr7 159138663 1295694 0.008141918347020423 0.18210470254714262 chr8 146364022 2006908 0.013711757661319254 0.1365138504095403 chr9 141213431 1027331 0.007275023294349388 0.09184290357914533 chr10 135534747 1178170 0.008692752420159829 0.13992603455129166 chr11 135006516 725155 0.005371259265737959 0.07989138904950355 chr12 133851895 1129327 0.008437138674801727 0.0980888630549066 chr13 115169878 624699 0.005424152659083307 0.07558627156528538 chr14 107349540 781922 0.00728388775583016 0.08803564675992542 chr15 102531392 587345 0.005728440710138803 0.07829170057526894 chr16 90354753 738268 0.008170771049531839 0.09427408099542046 chr17 81195210 1012746 0.012472977162076434 0.116057311243628 chr18 78077248 562118 0.007199510925385075 0.1120138620102926 chr19 59128983 479511 0.00810957631386963 0.1307688476466269 chr20 63025520 549791 0.008723307637921908 0.09751153720807548 chr21 48129895 186112 0.00386686902184183 0.06758827123556532 chr22 51304566 363687 0.007088784261424217 0.08640777615146569 chrMT 16571 31085 1.875867479331362 1.7125725225978956 chrX 155270560 842130 0.005423629566351793 0.07887133668736093 chrY 59373566 60337 0.0010162266487412934 0.04053579611990614