BamQC report ----------------------------------- >>>>>>> Input bam file = /Users/strigg/Desktop/20200429/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Users/strigg/Desktop/20200429/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats/genome_results.txt >>>>>>> Reference number of bases = 506,970,227 bp number of contigs = 21 >>>>>>> Globals number of windows = 420 number of reads = 78,560,122 number of mapped reads = 78,560,122 (100%) number of mapped paired reads (first in pair) = 39,280,061 number of mapped paired reads (second in pair) = 39,280,061 number of mapped paired reads (both in pair) = 78,560,122 number of mapped paired reads (singletons) = 0 number of mapped bases = 8,345,705,600 bp number of sequenced bases = 8,308,540,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,027,809 duplication rate = 47.24% >>>>>>> Insert size mean insert size = 144.6609 std insert size = 81.2184 median insert size = 128 >>>>>>> Mapping quality mean mapping quality = 18.0501 >>>>>>> ACTG content number of A's = 3,310,635,970 bp (39.85%) number of C's = 842,628,577 bp (10.14%) number of T's = 3,309,294,141 bp (39.83%) number of G's = 845,982,029 bp (10.18%) number of N's = 55,673 bp (0%) GC percentage = 20.32% >>>>>>> Mismatches and indels general error rate = 0.2176 number of mismatches = 1,723,794,603 number of insertions = 51,232,487 mapped reads with insertion percentage = 42.26% number of deletions = 22,505,941 mapped reads with deletion percentage = 23.69% homopolymer indels = 56.51% >>>>>>> Coverage mean coverageData = 16.4619X std coverageData = 61.5992X There is a 84.42% of reference with a coverageData >= 1X There is a 79.19% of reference with a coverageData >= 2X There is a 72.41% of reference with a coverageData >= 3X There is a 67.86% of reference with a coverageData >= 4X There is a 63.01% of reference with a coverageData >= 5X There is a 59.18% of reference with a coverageData >= 6X There is a 55.35% of reference with a coverageData >= 7X There is a 52.12% of reference with a coverageData >= 8X There is a 48.99% of reference with a coverageData >= 9X There is a 46.24% of reference with a coverageData >= 10X There is a 43.59% of reference with a coverageData >= 11X There is a 41.22% of reference with a coverageData >= 12X There is a 38.95% of reference with a coverageData >= 13X There is a 36.89% of reference with a coverageData >= 14X There is a 34.93% of reference with a coverageData >= 15X There is a 33.13% of reference with a coverageData >= 16X There is a 31.42% of reference with a coverageData >= 17X There is a 29.84% of reference with a coverageData >= 18X There is a 28.33% of reference with a coverageData >= 19X There is a 26.93% of reference with a coverageData >= 20X There is a 25.59% of reference with a coverageData >= 21X There is a 24.34% of reference with a coverageData >= 22X There is a 23.15% of reference with a coverageData >= 23X There is a 22.04% of reference with a coverageData >= 24X There is a 20.97% of reference with a coverageData >= 25X There is a 19.97% of reference with a coverageData >= 26X There is a 19.02% of reference with a coverageData >= 27X There is a 18.13% of reference with a coverageData >= 28X There is a 17.27% of reference with a coverageData >= 29X There is a 16.46% of reference with a coverageData >= 30X There is a 15.69% of reference with a coverageData >= 31X There is a 14.96% of reference with a coverageData >= 32X There is a 14.26% of reference with a coverageData >= 33X There is a 13.6% of reference with a coverageData >= 34X There is a 12.97% of reference with a coverageData >= 35X There is a 12.38% of reference with a coverageData >= 36X There is a 11.8% of reference with a coverageData >= 37X There is a 11.26% of reference with a coverageData >= 38X There is a 10.74% of reference with a coverageData >= 39X There is a 10.25% of reference with a coverageData >= 40X There is a 9.78% of reference with a coverageData >= 41X There is a 9.33% of reference with a coverageData >= 42X There is a 8.9% of reference with a coverageData >= 43X There is a 8.5% of reference with a coverageData >= 44X There is a 8.11% of reference with a coverageData >= 45X There is a 7.74% of reference with a coverageData >= 46X There is a 7.39% of reference with a coverageData >= 47X There is a 7.05% of reference with a coverageData >= 48X There is a 6.74% of reference with a coverageData >= 49X There is a 6.43% of reference with a coverageData >= 50X There is a 6.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig Cr_scaffold0000001 36897007 624817582 16.934099343071377 54.914319923191925 Cr_scaffold0000002 35124817 564360503 16.067286642375958 54.597525537577226 Cr_scaffold0000003 33138466 547480744 16.521004442390304 44.354379646334834 Cr_scaffold0000004 31456035 539156134 17.13999027531601 42.27154566693287 Cr_scaffold0000005 30612693 488397980 15.954100477210549 32.411681125896884 Cr_scaffold0000006 30259679 492505596 16.275968955255607 32.39457197903676 Cr_scaffold0000007 29872177 477042754 15.96946730732079 45.243432597445725 Cr_scaffold0000008 27803016 467043496 16.798303320762034 109.72986117447184 Cr_scaffold0000009 25126635 405353812 16.132435242522526 40.246550854497855 Cr_scaffold0000010 24815513 402306836 16.211908897470707 38.021533442623095 Cr_scaffold0000011 35794548 626880636 17.51329939967394 30.111669907268073 Cr_scaffold0000012 22957860 344899879 15.023171976830593 23.13582951088281 Cr_scaffold0000013 21502856 329115322 15.305656234688081 24.061140331670362 Cr_scaffold0000014 21148584 349238459 16.513562279157792 53.70054056457342 Cr_scaffold0000015 19091682 319360575 16.72773383717579 83.66025511894486 Cr_scaffold0000016 18525937 295706625 15.961763499465642 51.76494996258494 Cr_scaffold0000017 17562062 308487706 17.56557436137055 181.6498015635079 Cr_scaffold0000018 14680182 233233549 15.887646965139805 53.05253679976315 Cr_scaffold0000019 14290452 261793449 18.31946596230826 86.10021374381849 Cr_scaffold0000020 8286978 129928875 15.678679851690205 37.72862412432549 Cr_scaffold0000021 8023048 138595088 17.27461782604317 34.69833282578707