BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068126.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,075,431 number of mapped reads = 3,816,444 (93.65%) number of supplementary alignments = 22,010 (0.54%) number of secondary alignments = 0 number of mapped bases = 246,542,467 bp number of sequenced bases = 246,425,021 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 443,428 duplication rate = 9.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6998 >>>>>>> ACTG content number of A's = 64,181,927 bp (26.05%) number of C's = 44,480,803 bp (18.05%) number of T's = 79,752,642 bp (32.36%) number of G's = 57,981,782 bp (23.53%) number of N's = 27,867 bp (0.01%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,478,129 number of insertions = 17,395 mapped reads with insertion percentage = 0.45% number of deletions = 66,010 mapped reads with deletion percentage = 1.71% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.0796X std coverageData = 1.0632X There is a 6% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 18601700 0.07463050613623146 2.495387593895537 chr2 243199373 25399395 0.10443857106490155 1.2534504665361723 chr3 198022430 17313346 0.08743123695633874 0.3853708927648747 chr4 191154276 9853605 0.05154791828983203 0.3418460965182769 chr5 180915260 12270993 0.06782729660284047 0.34926552083817597 chr6 171115067 16180369 0.09455841197198608 0.5298854598129483 chr7 159138663 17518819 0.11008524685167174 1.7932116084662042 chr8 146364022 13078367 0.08935506705329538 1.1848133877132379 chr9 141213431 8718926 0.061742894696751614 0.8134924632862761 chr10 135534747 10789305 0.0796054535004223 0.6654208095822779 chr11 135006516 11002421 0.08149548129958409 0.5857214331679106 chr12 133851895 12652534 0.09452637185300963 0.4227302529201367 chr13 115169878 7368712 0.06398124342894589 0.3397271168592493 chr14 107349540 7334299 0.06832166211424846 0.41412296500032203 chr15 102531392 5719495 0.05578286696819643 0.380542622695011 chr16 90354753 7676069 0.0849547892627187 0.44669437800953604 chr17 81195210 5667925 0.06980614989480291 0.37780674588260305 chr18 78077248 7603141 0.09737972578131852 1.6141150630271304 chr19 59128983 5744700 0.09715540008526782 1.5908343764807114 chr20 63025520 5292881 0.08397996557584927 0.4143387364562051 chr21 48129895 5445596 0.11314373322443359 0.4621020555385663 chr22 51304566 2913426 0.056786875460558425 0.2996395885866645 chrMT 16571 155090 9.359121356586808 6.03662194166801 chrX 155270560 11229660 0.07232317575205499 0.4626055821229353 chrY 59373566 1011693 0.017039451529658838 0.43198923307398757