Saudi Arabia 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 Saudi Arabia chicken
Species taxonomy Gallus gallus domesticus
Classification Village
Region Saudi Arabia
Purpose Unclear
Description

This is the indigenous chicken ecotype of Saudi Arabia.

Characteristics

NA


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 149335 650455 22.9585% 13797 104154 13.2467%
exonic;splicing 32 188 17.0213% 0 0 0%
exonic_unknown 3 582 0.5155% 0 82 0%
frameshift_deletion 0 0 0% 701 15977 4.3876%
frameshift_insertion 0 0 0% 651 13308 4.8918%
intergenic 3370260 15129055 22.2767% 286520 2238383 12.8003%
intronic 4227323 17735594 23.8352% 378491 2641780 14.3271%
ncRNA_exonic 88553 400185 22.128% 7033 54342 12.9421%
ncRNA_exonic;splicing 68 231 29.4372% 6 43 13.9535%
ncRNA_intronic 842586 3728327 22.5996% 76116 575920 13.2164%
ncRNA_splicing 526 2341 22.469% 64 478 13.3891%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 435 8777 4.9561%
nonframeshift_insertion 0 0 0% 191 4784 3.9925%
nonsynonymous 39131 336233 11.6381% 0 0 0%
splice_acceptor 83 750 11.0667% 66 964 6.8465%
splice_donor 105 1076 9.7584% 32 763 4.194%
splice_donor_acceptor 0 0 0% 18 45 40%
splice_UTR5 65 400 16.25% 5 106 4.717%
splie_Others 0 0 0% 40 654 6.1162%
startloss 136 671 20.2683% 2 51 3.9216%
stopgain 425 4175 10.1796% 21 1252 1.6773%
stoploss 75 353 21.2465% 7 63 11.1111%
synonymous 90027 548813 16.4039% 0 0 0%
upstream 151779 679592 22.3338% 12240 98760 12.3937%
upstream;downstream 12638 57451 21.9979% 1086 9367 11.5939%
UTR3 73824 361040 20.4476% 7525 61415 12.2527%
UTR5 20386 112990 18.0423% 1429 16935 8.4381%
UTR5;UTR3 500 2524 19.8098% 48 381 12.5984%
Total 9067860 39753026 22.8105% 786525 5848802 13.4476%
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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