Taiwan 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 Taiwan Native chicken
Species taxonomy Gallus gallus domesticus
Classification Village
Region China
Purpose Unclear
Description

This is a indigenous ecotype in Taiwan Island.

Characteristics

NA


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 42809 650455 6.5814% 4058 104154 3.8962%
exonic;splicing 8 188 4.2553% 0 0 0%
exonic_unknown 0 582 0% 0 82 0%
frameshift_deletion 0 0 0% 248 15977 1.5522%
frameshift_insertion 0 0 0% 226 13308 1.6982%
intergenic 914530 15129055 6.0449% 81225 2238383 3.6287%
intronic 1182509 17735594 6.6674% 106694 2641780 4.0387%
ncRNA_exonic 24972 400185 6.2401% 2028 54342 3.7319%
ncRNA_exonic;splicing 14 231 6.0606% 2 43 4.6512%
ncRNA_intronic 241667 3728327 6.4819% 22402 575920 3.8898%
ncRNA_splicing 160 2341 6.8347% 11 478 2.3013%
ncRNA_UTR5 0 0 0% 0 18 0%
nonframeshift_deletion 0 0 0% 126 8777 1.4356%
nonframeshift_insertion 0 0 0% 50 4784 1.0452%
nonsynonymous 11142 336233 3.3138% 0 0 0%
splice_acceptor 22 750 2.9333% 19 964 1.971%
splice_donor 28 1076 2.6022% 11 763 1.4417%
splice_donor_acceptor 0 0 0% 8 45 17.7778%
splice_UTR5 21 400 5.25% 2 106 1.8868%
splie_Others 0 0 0% 13 654 1.9878%
startloss 38 671 5.6632% 3 51 5.8824%
stopgain 132 4175 3.1617% 5 1252 0.3994%
stoploss 19 353 5.3824% 1 63 1.5873%
synonymous 25974 548813 4.7328% 0 0 0%
upstream 41689 679592 6.1344% 3408 98760 3.4508%
upstream;downstream 3716 57451 6.4681% 313 9367 3.3415%
UTR3 22307 361040 6.1785% 2269 61415 3.6945%
UTR5 5525 112990 4.8898% 399 16935 2.3561%
UTR5;UTR3 149 2524 5.9033% 8 381 2.0997%
Total 2517431 39753026 6.3327% 223529 5848802 3.8218%
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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