Lari
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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 Lari
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region Afghanistan, Pakistan, Iran
Purpose Fighting
Description

Lari is the largest breed of Asil/Assel in Pakistan, Iran, and Afghanistan. The height is 32-36 inches and weight is 10-12 pounds for the rooster. Over hundreds of years of selective breeding, Lari is very aggressive and is used in cockfighting. It is proposed to have ancestry from Malay breed.

Characteristics

NA


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 159255 650455 24.4836% 14021 104154 13.4618%
exonic;splicing 29 188 15.4255% 0 0 0%
exonic_unknown 0 582 0% 0 82 0%
frameshift_deletion 0 0 0% 464 15977 2.9042%
frameshift_insertion 0 0 0% 420 13308 3.156%
intergenic 3746782 15129055 24.7655% 308380 2238383 13.7769%
intronic 4699750 17735594 26.499% 410505 2641780 15.539%
ncRNA_exonic 97670 400185 24.4062% 7486 54342 13.7757%
ncRNA_exonic;splicing 68 231 29.4372% 5 43 11.6279%
ncRNA_intronic 952620 3728327 25.5509% 84352 575920 14.6465%
ncRNA_splicing 593 2341 25.3311% 69 478 14.4351%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 353 8777 4.0219%
nonframeshift_insertion 0 0 0% 142 4784 2.9682%
nonsynonymous 35201 336233 10.4692% 0 0 0%
splice_acceptor 86 750 11.4667% 66 964 6.8465%
splice_donor 108 1076 10.0372% 23 763 3.0144%
splice_donor_acceptor 0 0 0% 15 45 33.3333%
splice_UTR5 59 400 14.75% 7 106 6.6038%
splie_Others 0 0 0% 39 654 5.9633%
startloss 108 671 16.0954% 0 51 0%
stopgain 333 4175 7.976% 20 1252 1.5974%
stoploss 59 353 16.7139% 9 63 14.2857%
synonymous 88790 548813 16.1786% 0 0 0%
upstream 141871 679592 20.8759% 10599 98760 10.7321%
upstream;downstream 10255 57451 17.85% 796 9367 8.4979%
UTR3 80017 361040 22.1629% 7836 61415 12.7591%
UTR5 15985 112990 14.1473% 1030 16935 6.0821%
UTR5;UTR3 427 2524 16.9176% 39 381 10.2362%
Total 10030066 39753026 25.2309% 846677 5848802 14.4761%
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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