Yunyang Black-bone 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 Yunyang Black-bone chicken
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region China
Purpose Dual
Description

The Yunyang Black-bone chickens are also known as Black chickens, Black-bone chickens, and Medicinal chickens. The origin and mainly distribution area of this breed is Yunyang District of Hubei Province, China.

Characteristics

Yunyang Black-bone chicken is a dual-purpose local breed. The body size of Yunyang Black-bone chicken is small. The wing feathers are developed, and the tail feathers are upturned, they have the flying ability. The feathers are pure white. The beak is short and curved in black olor, the comb and wattles are black, shanks are black. Its appearance characteristics can be summarized as white feather, single comb, green ear, upturned tail, glabrous shank, four toes, black skin, black meat and black bone.The rooster has white, shiny plumage and a thin, long wattles. Hen has a thin neck, long body, its ears are green with some milky white. The hens start laying at around 200 days and lay about 160 eggs a year.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 140475 650455 21.5964% 12643 104154 12.1388%
exonic;splicing 26 188 13.8298% 0 0 0%
exonic_unknown 12 582 2.0619% 0 82 0%
frameshift_deletion 0 0 0% 745 15977 4.663%
frameshift_insertion 0 0 0% 641 13308 4.8167%
intergenic 3189778 15129055 21.0838% 260566 2238383 11.6408%
intronic 3992830 17735594 22.5131% 343749 2641780 13.012%
ncRNA_exonic 83916 400185 20.9693% 6410 54342 11.7957%
ncRNA_exonic;splicing 57 231 24.6753% 6 43 13.9535%
ncRNA_intronic 803054 3728327 21.5393% 70082 575920 12.1687%
ncRNA_splicing 473 2341 20.205% 63 478 13.1799%
ncRNA_UTR5 0 0 0% 2 18 11.1111%
nonframeshift_deletion 0 0 0% 421 8777 4.7966%
nonframeshift_insertion 0 0 0% 206 4784 4.306%
nonsynonymous 37097 336233 11.0331% 0 0 0%
splice_acceptor 83 750 11.0667% 72 964 7.4689%
splice_donor 106 1076 9.8513% 22 763 2.8834%
splice_donor_acceptor 0 0 0% 15 45 33.3333%
splice_UTR5 62 400 15.5% 5 106 4.717%
splie_Others 0 0 0% 27 654 4.1284%
startloss 128 671 19.076% 3 51 5.8824%
stopgain 399 4175 9.5569% 17 1252 1.3578%
stoploss 68 353 19.2635% 5 63 7.9365%
synonymous 84023 548813 15.31% 0 0 0%
upstream 143772 679592 21.1556% 11572 98760 11.7173%
upstream;downstream 12170 57451 21.1833% 1013 9367 10.8146%
UTR3 70294 361040 19.4699% 6754 61415 10.9973%
UTR5 20289 112990 17.9565% 1557 16935 9.194%
UTR5;UTR3 494 2524 19.5721% 37 381 9.7113%
Total 8579606 39753026 21.5823% 716633 5848802 12.2526%
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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