BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004147.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 = 2,674,892 number of mapped reads = 2,005,516 (74.98%) number of supplementary alignments = 8,960 (0.33%) number of secondary alignments = 0 number of mapped bases = 127,990,660 bp number of sequenced bases = 127,925,595 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 323,538 duplication rate = 12.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4717 >>>>>>> ACTG content number of A's = 33,938,689 bp (26.53%) number of C's = 22,094,451 bp (17.27%) number of T's = 42,943,581 bp (33.57%) number of G's = 28,936,519 bp (22.62%) number of N's = 12,355 bp (0.01%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,287,722 number of insertions = 10,707 mapped reads with insertion percentage = 0.53% number of deletions = 39,388 mapped reads with deletion percentage = 1.94% homopolymer indels = 49.65% >>>>>>> Coverage mean coverageData = 0.0413X std coverageData = 0.4202X There is a 2.3% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 12334498 0.04948632806014152 0.5875361201376634 chr2 243199373 12270058 0.05045267119171397 0.5438609595983989 chr3 198022430 8436243 0.042602461751428865 0.3357580540629874 chr4 191154276 8282167 0.04332713436135742 0.341135998366978 chr5 180915260 7786200 0.04303782887082051 0.3346543251976817 chr6 171115067 8705177 0.05087323490923216 0.4162214216213579 chr7 159138663 6946282 0.04364924191929399 0.556674044260765 chr8 146364022 7615635 0.052032151726467316 0.5094287182083822 chr9 141213431 4694192 0.03324182386022474 0.3911216148573552 chr10 135534747 5310154 0.039179281457617655 0.3507767165714161 chr11 135006516 4750904 0.035190182968650195 0.39692120792129576 chr12 133851895 5321596 0.03975734523594156 0.3205828806277305 chr13 115169878 3170914 0.027532494216934048 0.26869284011894573 chr14 107349540 3235918 0.03014375282837728 0.3013007792398833 chr15 102531392 3316012 0.03234143158809353 0.28655063865972835 chr16 90354753 3818218 0.04225807578711437 0.3342578463133198 chr17 81195210 2988633 0.03680799643230186 0.3256442306276799 chr18 78077248 3555757 0.04554152574639926 0.7024794866215609 chr19 59128983 2132020 0.03605710586972213 0.44047701130982886 chr20 63025520 3255882 0.051659740371836675 0.37026133074237827 chr21 48129895 1951894 0.040554711370137 0.33660688101161435 chr22 51304566 1354162 0.02639457080681669 0.25026876792659075 chrMT 16571 82797 4.996499909480417 5.725372486444762 chrX 155270560 6405754 0.04125543180883742 0.35127503656736486 chrY 59373566 269593 0.004540623347433772 0.10590361146477961