BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525064.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 = 557,886 number of mapped reads = 485,435 (87.01%) number of supplementary alignments = 1,542 (0.28%) number of secondary alignments = 0 number of mapped bases = 28,185,551 bp number of sequenced bases = 28,176,535 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,025 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1756 >>>>>>> ACTG content number of A's = 7,279,907 bp (25.84%) number of C's = 5,370,763 bp (19.06%) number of T's = 8,981,001 bp (31.87%) number of G's = 6,541,811 bp (23.22%) number of N's = 3,053 bp (0.01%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 135,127 number of insertions = 2,159 mapped reads with insertion percentage = 0.44% number of deletions = 5,624 mapped reads with deletion percentage = 1.15% homopolymer indels = 44.66% >>>>>>> Coverage mean coverageData = 0.0091X std coverageData = 0.1169X There is a 0.85% of reference with a coverageData >= 1X There is a 0.04% 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 2270411 0.009108948218026706 0.17166105269794407 chr2 243199373 2410852 0.009913068320287158 0.13404173162903824 chr3 198022430 1885868 0.009523507008776733 0.10236690494006238 chr4 191154276 1854299 0.009700536335373424 0.10853092161564802 chr5 180915260 1717699 0.009494494825920158 0.10208874739538377 chr6 171115067 1647518 0.009628129356954873 0.1057930319883191 chr7 159138663 1552383 0.009754907894381392 0.13039939709130657 chr8 146364022 1404962 0.009599093963132552 0.12023624078286263 chr9 141213431 1176145 0.00832884656700962 0.10372527846954728 chr10 135534747 1364404 0.010066820724577735 0.13347917560026762 chr11 135006516 1285132 0.009519036844117954 0.1074590883347464 chr12 133851895 1248348 0.009326337890098605 0.10211719917016268 chr13 115169878 890699 0.0077337843494112235 0.09194390132524023 chr14 107349540 844771 0.007869349044253007 0.09320429938107633 chr15 102531392 809544 0.007895572119024776 0.0929675854909256 chr16 90354753 806921 0.008930587193348865 0.10219736607828081 chr17 81195210 727927 0.008965147081952249 0.10048661634693572 chr18 78077248 748021 0.009580524661934806 0.14154101929675586 chr19 59128983 541764 0.009162410251500521 0.13349963327537956 chr20 63025520 590454 0.00936849073200824 0.1024238815014307 chr21 48129895 372592 0.007741384019225473 0.09552189175257322 chr22 51304566 324942 0.006333588320384584 0.08320896006937072 chrMT 16571 5655 0.3412588256592843 0.6321762056146604 chrX 155270560 1611092 0.010376030072925608 0.1105832987140896 chrY 59373566 93148 0.001568846311168172 0.06266592296117923