BamQC report ----------------------------------- >>>>>>> Input bam file = /Users/strigg/Desktop/20200427/Sealice_F1_S20.dedup.sorted.bam outfile = /Users/strigg/Desktop/20200427/Sealice_F1_S20.dedup.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 = 79,611,238 number of mapped reads = 79,611,238 (100%) number of mapped paired reads (first in pair) = 39,805,619 number of mapped paired reads (second in pair) = 39,805,619 number of mapped paired reads (both in pair) = 79,611,238 number of mapped paired reads (singletons) = 0 number of mapped bases = 9,519,638,551 bp number of sequenced bases = 9,475,215,166 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,313,082 duplication rate = 26.13% >>>>>>> Insert size mean insert size = 156.8953 std insert size = 77.1376 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 15.8508 >>>>>>> ACTG content number of A's = 3,762,018,572 bp (39.7%) number of C's = 975,929,878 bp (10.3%) number of T's = 3,759,461,175 bp (39.68%) number of G's = 977,805,541 bp (10.32%) number of N's = 65,145 bp (0%) GC percentage = 20.62% >>>>>>> Mismatches and indels general error rate = 0.2237 number of mismatches = 2,010,625,717 number of insertions = 61,265,857 mapped reads with insertion percentage = 47.51% number of deletions = 26,451,178 mapped reads with deletion percentage = 26.85% homopolymer indels = 55.57% >>>>>>> Coverage mean coverageData = 18.7775X std coverageData = 66.3745X There is a 84.86% of reference with a coverageData >= 1X There is a 79.84% of reference with a coverageData >= 2X There is a 73.64% of reference with a coverageData >= 3X There is a 69.37% of reference with a coverageData >= 4X There is a 64.88% of reference with a coverageData >= 5X There is a 61.27% of reference with a coverageData >= 6X There is a 57.66% of reference with a coverageData >= 7X There is a 54.6% of reference with a coverageData >= 8X There is a 51.6% of reference with a coverageData >= 9X There is a 48.95% of reference with a coverageData >= 10X There is a 46.41% of reference with a coverageData >= 11X There is a 44.11% of reference with a coverageData >= 12X There is a 41.9% of reference with a coverageData >= 13X There is a 39.89% of reference with a coverageData >= 14X There is a 37.96% of reference with a coverageData >= 15X There is a 36.18% of reference with a coverageData >= 16X There is a 34.49% of reference with a coverageData >= 17X There is a 32.91% of reference with a coverageData >= 18X There is a 31.41% of reference with a coverageData >= 19X There is a 30% of reference with a coverageData >= 20X There is a 28.66% of reference with a coverageData >= 21X There is a 27.4% of reference with a coverageData >= 22X There is a 26.19% of reference with a coverageData >= 23X There is a 25.06% of reference with a coverageData >= 24X There is a 23.97% of reference with a coverageData >= 25X There is a 22.95% of reference with a coverageData >= 26X There is a 21.97% of reference with a coverageData >= 27X There is a 21.05% of reference with a coverageData >= 28X There is a 20.16% of reference with a coverageData >= 29X There is a 19.32% of reference with a coverageData >= 30X There is a 18.52% of reference with a coverageData >= 31X There is a 17.75% of reference with a coverageData >= 32X There is a 17.02% of reference with a coverageData >= 33X There is a 16.32% of reference with a coverageData >= 34X There is a 15.66% of reference with a coverageData >= 35X There is a 15.02% of reference with a coverageData >= 36X There is a 14.41% of reference with a coverageData >= 37X There is a 13.83% of reference with a coverageData >= 38X There is a 13.27% of reference with a coverageData >= 39X There is a 12.73% of reference with a coverageData >= 40X There is a 12.22% of reference with a coverageData >= 41X There is a 11.73% of reference with a coverageData >= 42X There is a 11.26% of reference with a coverageData >= 43X There is a 10.81% of reference with a coverageData >= 44X There is a 10.38% of reference with a coverageData >= 45X There is a 9.97% of reference with a coverageData >= 46X There is a 9.57% of reference with a coverageData >= 47X There is a 9.2% of reference with a coverageData >= 48X There is a 8.83% of reference with a coverageData >= 49X There is a 8.48% of reference with a coverageData >= 50X There is a 8.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig Cr_scaffold0000001 36897007 714865995 19.374633693188176 61.50533575558041 Cr_scaffold0000002 35124817 641967240 18.27674262331388 58.75358823617906 Cr_scaffold0000003 33138466 627780647 18.944167391453785 48.56295140384845 Cr_scaffold0000004 31456035 618598046 19.665480598556048 45.70812994414097 Cr_scaffold0000005 30612693 559909539 18.290110543361866 37.25561122970588 Cr_scaffold0000006 30259679 562698673 18.595659028636753 37.75512238948376 Cr_scaffold0000007 29872177 543795664 18.204085494003333 49.704877735361684 Cr_scaffold0000008 27803016 528560298 19.01089788244556 119.76168593439063 Cr_scaffold0000009 25126635 464855308 18.500499887867992 44.831399792130085 Cr_scaffold0000010 24815513 459153774 18.502691199654024 40.79543663742039 Cr_scaffold0000011 35794548 716142100 20.00701615229224 33.15388163287119 Cr_scaffold0000012 22957860 391884456 17.069729321461146 27.208740622639233 Cr_scaffold0000013 21502856 375800495 17.476771225180507 28.65490080827524 Cr_scaffold0000014 21148584 396498264 18.748218036725294 59.94416124524074 Cr_scaffold0000015 19091682 364697101 19.102408106315618 89.14827854900084 Cr_scaffold0000016 18525937 336209263 18.14803013742301 50.16229154522443 Cr_scaffold0000017 17562062 348705035 19.855586149280192 185.51724384000576 Cr_scaffold0000018 14680182 266125712 18.12822974538054 61.62752870243768 Cr_scaffold0000019 14290452 295773645 20.69729110037947 99.74464885938873 Cr_scaffold0000020 8286978 146920877 17.729125985371265 41.55257079157297 Cr_scaffold0000021 8023048 158696419 19.780066004840055 40.966541095895174