BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524978.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 = 1,823,313 number of mapped reads = 1,697,039 (93.07%) number of supplementary alignments = 7,341 (0.4%) number of secondary alignments = 0 number of mapped bases = 101,619,425 bp number of sequenced bases = 101,593,663 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,045 duplication rate = 5.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5964 >>>>>>> ACTG content number of A's = 26,639,450 bp (26.22%) number of C's = 20,343,164 bp (20.02%) number of T's = 31,097,081 bp (30.61%) number of G's = 23,510,857 bp (23.14%) number of N's = 3,111 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 473,969 number of insertions = 7,606 mapped reads with insertion percentage = 0.45% number of deletions = 15,738 mapped reads with deletion percentage = 0.92% homopolymer indels = 41.85% >>>>>>> Coverage mean coverageData = 0.0328X std coverageData = 0.355X There is a 2.64% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 7572854 0.030382487993881466 0.728253917566012 chr2 243199373 7962240 0.032739558090883726 0.3144396588875246 chr3 198022430 6296630 0.031797559498689114 0.21054928756235267 chr4 191154276 6190669 0.03238572073585212 0.23072474623959063 chr5 180915260 5542602 0.030636453773993415 0.21212290504609854 chr6 171115067 5288497 0.030906086136763163 0.22628430897649435 chr7 159138663 6415516 0.040313999621826656 0.43125472633636464 chr8 146364022 4150427 0.02835687994417098 0.5023291473492546 chr9 141213431 4906859 0.03474782083582404 0.2959072539474218 chr10 135534747 4055743 0.02992400908085954 0.3761339092322276 chr11 135006516 3545408 0.026261013949874835 0.24318620429028448 chr12 133851895 7098247 0.05303060520734503 0.30882492027637276 chr13 115169878 3722545 0.032322210152901265 0.21475568765841674 chr14 107349540 3663733 0.03412900511730185 0.23527460979454642 chr15 102531392 2740668 0.026730037957545725 0.19252257931412015 chr16 90354753 3121719 0.034549582577022814 0.23976647102181958 chr17 81195210 3068795 0.03779527142056779 0.24091381897207398 chr18 78077248 3263439 0.04179756694293323 0.51108339443197 chr19 59128983 1764522 0.029841913567158766 0.4924515016173053 chr20 63025520 3604127 0.05718520053464057 0.29796316652319305 chr21 48129895 1248622 0.025942753459154647 0.2123819954524645 chr22 51304566 1035256 0.020178632833576644 0.1685136166448787 chrMT 16571 50292 3.0349405588075555 3.2811295725338714 chrX 155270560 5032689 0.03241238390587372 0.24318367069244853 chrY 59373566 277326 0.004670866493011385 0.10911419290849