BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714220.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 136,618 number of mapped reads = 82,136 (60.12%) number of supplementary alignments = 2,022 (1.48%) number of secondary alignments = 0 number of mapped bases = 10,235,380 bp number of sequenced bases = 10,005,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,510 duplication rate = 41.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9225 >>>>>>> ACTG content number of A's = 2,560,904 bp (25.6%) number of C's = 2,058,631 bp (20.58%) number of T's = 2,402,864 bp (24.02%) number of G's = 2,982,744 bp (29.81%) number of N's = 90 bp (0%) GC percentage = 50.39% >>>>>>> Mismatches and indels general error rate = 0.0448 number of mismatches = 420,250 number of insertions = 10,583 mapped reads with insertion percentage = 12.29% number of deletions = 34,343 mapped reads with deletion percentage = 39.61% homopolymer indels = 29.76% >>>>>>> Coverage mean coverageData = 0.0033X std coverageData = 1.3983X There is a 0.02% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 768256 0.0030822631330575502 0.943392487685915 chr2 243199373 1609935 0.006619815586448901 4.067745368543265 chr3 198022430 393046 0.0019848559579841536 0.4405302593684455 chr4 191154276 356846 0.0018667958021509287 0.5391382408057368 chr5 180915260 578904 0.0031998627423689965 0.8124347273418848 chr6 171115067 518654 0.0030310247314457705 0.6019784186118408 chr7 159138663 269346 0.0016925239594353008 0.23901139367019886 chr8 146364022 331021 0.0022616282025920277 0.3853442791675775 chr9 141213431 324391 0.002297168178004258 0.47875154321283825 chr10 135534747 559349 0.004126978596861217 0.7506649439531076 chr11 135006516 376451 0.002788391339570603 0.5306428751342577 chr12 133851895 608505 0.004546106724899188 1.0134867388936937 chr13 115169878 290554 0.0025228297975621716 0.5199750310255132 chr14 107349540 568662 0.0052972933093146 2.9428614448309864 chr15 102531392 273600 0.0026684510437544827 0.4034295091695133 chr16 90354753 175047 0.0019373302918552608 0.2671498569516404 chr17 81195210 204356 0.0025168479766232515 0.4037413773641523 chr18 78077248 316147 0.004049156548140631 0.830384325526945 chr19 59128983 207922 0.003516414276903765 0.424223463156584 chr20 63025520 241594 0.0038332726171874504 0.5935772695140603 chr21 48129895 115248 0.002394520079464125 0.5244705235349738 chr22 51304566 54026 0.0010530446744252742 0.1457570378415069 chrMT 16571 62925 3.797296481805564 31.207919393192665 chrX 155270560 960631 0.00618681996123412 0.7932667595648799 chrY 59373566 69964 0.00117836951211588 0.2688666351831853