Kenya Native chicken
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Background Information Variants Annotation&Density Genetic Differentiation
Genetic Affinity ADMIXTURE Analysis Runs of Homozygosity
Linkage Disequilibrium Decay Demographic History Selection

Background Information

Breed Card
Breed Kenya Native chicken
Species taxonomy Gallus gallus domesticus
Classification Village
Region Kenya
Purpose Unclear
Description

It refers to local village chickens collected in Kenya.

Characteristics

NA


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 168591 650455 25.9189% 13663 104154 13.1181%
exonic;splicing 29 188 15.4255% 0 0 0%
exonic_unknown 1 582 0.1718% 0 82 0%
frameshift_deletion 0 0 0% 638 15977 3.9932%
frameshift_insertion 0 0 0% 541 13308 4.0652%
intergenic 3825767 15129055 25.2875% 282849 2238383 12.6363%
intronic 4825321 17735594 27.207% 382858 2641780 14.4924%
ncRNA_exonic 101846 400185 25.4497% 7010 54342 12.8998%
ncRNA_exonic;splicing 69 231 29.8701% 4 43 9.3023%
ncRNA_intronic 967139 3728327 25.9403% 76627 575920 13.3051%
ncRNA_splicing 590 2341 25.2029% 73 478 15.272%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 391 8777 4.4548%
nonframeshift_insertion 0 0 0% 199 4784 4.1597%
nonsynonymous 43294 336233 12.8762% 0 0 0%
splice_acceptor 90 750 12% 70 964 7.2614%
splice_donor 125 1076 11.6171% 30 763 3.9318%
splice_donor_acceptor 0 0 0% 10 45 22.2222%
splice_UTR5 77 400 19.25% 7 106 6.6038%
splie_Others 0 0 0% 41 654 6.2691%
startloss 148 671 22.0566% 2 51 3.9216%
stopgain 419 4175 10.0359% 14 1252 1.1182%
stoploss 73 353 20.6799% 6 63 9.5238%
synonymous 102762 548813 18.7244% 0 0 0%
upstream 173189 679592 25.4843% 12189 98760 12.342%
upstream;downstream 14114 57451 24.567% 1089 9367 11.6259%
UTR3 83545 361040 23.1401% 7355 61415 11.9759%
UTR5 23602 112990 20.8886% 1474 16935 8.7039%
UTR5;UTR3 551 2524 21.8304% 50 381 13.1234%
Total 10331342 39753026 25.9888% 787191 5848802 13.459%
SNP Density
SNP_Annotation
INDEL Density
INDEL_Annotation

Genetic Differentiation

Summary

Genetic affinities of target population in the context of worldwide populations are measured by pairwise FST between target population and references. Smaller FST value indicates closer relationship. Regions represented by different colors are indicated above.

Genetic Affinity

PCA for G.gallus without G.g.bankiva , G.g.jabouillei, and some G.g.gallus

Summary

Genetic affiliation and population structure are shown by PCA plots. After removing G. g. bankiva, G. g. jabouillei, and some G. g. gallus individuals as outliers to other Red Jungle Fowl, the dataset contains 1,915 samples from domestic chicken and Red Jungle Fowl. User can add any populations with interests to show with the target population under this PCA context by using the item of “Add”.

ADMIXTURE Analysis

Summary

The inference of populations and individual ancestries is revealed by ADMIXTURE clustering. Length of each colored bar represents the proportion of proposed ancestry in the sample. User can add any populations with interests to compare with the target population by using the item of “Add”. The number of proposed ancestries is determined by “which K”.

Runs of Homozygosity

Summary

Runs of homozygosity (ROH) indicates long tracts of homozygous genotypes inherited from identical haplotypes of a common ancestor. Larger populations have fewer, shorter ROH, whereas isolated or bottlenecked populations have more, somewhat longer ROH. Admixture brings the fewest ROH, whereas inbreeding causes long ROH. The level of ROH is measured by number and length. The length of ROH can be defined in “ROH range”. User can add any populations with interests to compare with the target population by using the item of “Add”.

Linkage Disequilibrium Decay

Summary

Linkage disequilibrium (LD) decay is characterized by squared correlations (r²) of all SNPs frequencies against the physical distances between SNPs. User can add any populations with interests to compare with the target population by using the item of “Add”.

Demographic History

Summary

The changes of effective population size through time is inferred by SMC++. User can add any populations with interests to compare with the target population by using the item of “Add”.

Selection

Summary

Selective signals of the target population are detected by different methods. X axis indicates physical position of specific chromosomal region with interests which can be defined by “Region”. The gene annotation is shown below. Y axis of left (YL) indicates the values of Pi-ratio of -log2(πRJF/πTarget) or composite likelihood ratio (CLR) of SweeD. The levels of statistical significance are noted with different colors. Y axis of right (YR) shows the values of Fst (Target vs. Red Jungle Fowl), Pi, or Tajima’s D with blue line with sliding window approach. The genomic window size and step size for Tajima’s D are 5 kb and 5 kb, respectively. The genomic window size and step size for Fst and Pi are 10 kb and 5 kb, respectively. The methods are defined by “Method-YL” and “Method-YR”.

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