BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004128.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 = 3,296,544 number of mapped reads = 2,419,198 (73.39%) number of supplementary alignments = 15,688 (0.48%) number of secondary alignments = 0 number of mapped bases = 159,588,624 bp number of sequenced bases = 159,510,567 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 339,326 duplication rate = 10.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4515 >>>>>>> ACTG content number of A's = 43,353,022 bp (27.18%) number of C's = 29,429,501 bp (18.45%) number of T's = 51,525,116 bp (32.3%) number of G's = 35,181,841 bp (22.06%) number of N's = 21,087 bp (0.01%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,599,700 number of insertions = 13,410 mapped reads with insertion percentage = 0.55% number of deletions = 47,634 mapped reads with deletion percentage = 1.94% homopolymer indels = 47.35% >>>>>>> Coverage mean coverageData = 0.0516X std coverageData = 0.5409X There is a 2.5% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 14054670 0.05638770304207186 0.8707302162850924 chr2 243199373 13360277 0.05493549113714204 0.5982104887431304 chr3 198022430 10538539 0.05321891565516088 0.4377766052401894 chr4 191154276 10391759 0.05436320451445198 0.45488514733441004 chr5 180915260 9724506 0.053751717793181185 0.4392189045917915 chr6 171115067 9175740 0.053623214839403945 0.4722233806188091 chr7 159138663 9536151 0.05992353347847342 0.6899838994817327 chr8 146364022 9830980 0.0671680093623008 0.6225199182101923 chr9 141213431 6453195 0.04569816733650498 0.5017889148039517 chr10 135534747 7584454 0.055959480265234125 0.5430558739908621 chr11 135006516 6870923 0.05089326947745248 0.4844142741555623 chr12 133851895 6983870 0.0521761010555734 0.430580798316333 chr13 115169878 5162023 0.04482094701880295 0.40594224329661677 chr14 107349540 4352656 0.0405465733714369 0.3882607979262298 chr15 102531392 4283479 0.04177724418293277 0.3835771245424363 chr16 90354753 4136810 0.04578408841425309 0.4235045415974048 chr17 81195210 3684835 0.04538241849488412 0.41786536117346024 chr18 78077248 4379969 0.0560978916674932 0.7963919456271522 chr19 59128983 2720870 0.046015843025745934 0.6003542785309022 chr20 63025520 3376329 0.053570823374404525 0.4431844426527734 chr21 48129895 2134161 0.04434169241383136 0.4073724347771756 chr22 51304566 1609101 0.03136369967538562 0.33352453552650363 chrMT 16571 119138 7.189548005551868 6.338914452747276 chrX 155270560 8654155 0.05573596823506014 0.459781816493404 chrY 59373566 470034 0.007916553302525236 0.1994933977744502