BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525223.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 = 686,665 number of mapped reads = 634,867 (92.46%) number of supplementary alignments = 2,480 (0.36%) number of secondary alignments = 0 number of mapped bases = 39,440,967 bp number of sequenced bases = 39,427,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,917 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6325 >>>>>>> ACTG content number of A's = 10,817,541 bp (27.44%) number of C's = 7,886,477 bp (20%) number of T's = 11,972,241 bp (30.37%) number of G's = 8,749,791 bp (22.19%) number of N's = 1,059 bp (0%) GC percentage = 42.19% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 191,024 number of insertions = 3,224 mapped reads with insertion percentage = 0.5% number of deletions = 8,404 mapped reads with deletion percentage = 1.31% homopolymer indels = 42.55% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 0.1523X There is a 1.2% of reference with a coverageData >= 1X There is a 0.05% 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 3206797 0.012865753301372919 0.26678615217435153 chr2 243199373 3377000 0.013885726588612545 0.1617106448241465 chr3 198022430 2588172 0.013070095140232347 0.11874523444828136 chr4 191154276 2517932 0.013172250460146652 0.1251843730908644 chr5 180915260 2364505 0.013069682457964022 0.11878099676465921 chr6 171115067 2259088 0.013202157119220834 0.12372074435266368 chr7 159138663 2212540 0.01390322099162037 0.20042428935500356 chr8 146364022 2013508 0.013756850710210737 0.1445740040211487 chr9 141213431 1672057 0.01184063716998704 0.13199717382593593 chr10 135534747 1937134 0.01429252677175101 0.15754000831302203 chr11 135006516 1768628 0.013100315839570291 0.13238875605309844 chr12 133851895 1788533 0.013362029726960533 0.12121849178155948 chr13 115169878 1210592 0.010511359576155841 0.10634845438457473 chr14 107349540 1181523 0.011006316375459084 0.11145762802304128 chr15 102531392 1128431 0.011005712279805974 0.10859164053206335 chr16 90354753 1164883 0.012892326760054338 0.12431007302517758 chr17 81195210 1060783 0.013064600731988993 0.12184591963176103 chr18 78077248 1038538 0.0133014165663216 0.2097217090491507 chr19 59128983 808792 0.013678435835772789 0.19333013340546853 chr20 63025520 849262 0.013474890806136943 0.1207744860013488 chr21 48129895 523652 0.01087997387070967 0.11836733420577365 chr22 51304566 461440 0.008994131243601202 0.09839785289507859 chrMT 16571 2362 0.14253816909057992 0.3917658338421718 chrX 155270560 2170225 0.013977053988856613 0.1273591024487413 chrY 59373566 134590 0.002266833694981366 0.08271937084336707