Surena
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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 Surena
Species taxonomy Gallus gallus domesticus
Classification Village
Region Spain
Purpose Unclear
Description

This is indigenous chicken breed of Spain.

Characteristics

NA


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 96388 650455 14.8186% 8609 104154 8.2656%
exonic;splicing 29 188 15.4255% 0 0 0%
exonic_unknown 26 582 4.4674% 0 82 0%
frameshift_deletion 0 0 0% 1504 15977 9.4135%
frameshift_insertion 0 0 0% 1416 13308 10.6402%
intergenic 2314515 15129055 15.2985% 190219 2238383 8.4981%
intronic 2917947 17735594 16.4525% 250016 2641780 9.4639%
ncRNA_exonic 59854 400185 14.9566% 4492 54342 8.2662%
ncRNA_exonic;splicing 40 231 17.316% 1 43 2.3256%
ncRNA_intronic 591027 3728327 15.8523% 51681 575920 8.9736%
ncRNA_splicing 353 2341 15.079% 47 478 9.8326%
ncRNA_UTR5 0 0 0% 0 18 0%
nonframeshift_deletion 0 0 0% 458 8777 5.2182%
nonframeshift_insertion 0 0 0% 376 4784 7.8595%
nonsynonymous 31225 336233 9.2867% 0 0 0%
splice_acceptor 50 750 6.6667% 55 964 5.7054%
splice_donor 71 1076 6.5985% 23 763 3.0144%
splice_donor_acceptor 0 0 0% 9 45 20%
splice_UTR5 40 400 10% 3 106 2.8302%
splie_Others 0 0 0% 28 654 4.2813%
startloss 67 671 9.9851% 2 51 3.9216%
stopgain 263 4175 6.2994% 48 1252 3.8339%
stoploss 47 353 13.3144% 6 63 9.5238%
synonymous 100588 548813 18.3283% 0 0 0%
upstream 87274 679592 12.8421% 6662 98760 6.7456%
upstream;downstream 6181 57451 10.7587% 534 9367 5.7009%
UTR3 47430 361040 13.137% 4823 61415 7.8531%
UTR5 10104 112990 8.9424% 766 16935 4.5232%
UTR5;UTR3 246 2524 9.7464% 28 381 7.3491%
Total 6263765 39753026 15.7567% 521806 5848802 8.9216%
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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