Emei Black 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 Emei Black chicken
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region China
Purpose Dual
Description

Emei black chicken is a local breed used for meat and eggs. The origin and distribution area of Emei black chicken is Emei City, Sichuan Province, China. In 2006, about 10,000 chickens were raised in Emei. Emei black chickens are in a state of endangered and currently maintained.

Characteristics

Emei black chickens have large bodies, they have black feathers. Most of them have red single comb, a few have red or purple single comb or bean comb. Their wattles, ears and faces are red, but a few are purple and their beaks are black. Some of them have shank feathers, and the shank toes are black, their skins are white. The hens start laying at about 186 days and lay about 120 eggs a year.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 113591 650455 17.4633% 9372 104154 8.9982%
exonic;splicing 27 188 14.3617% 0 0 0%
exonic_unknown 17 582 2.921% 3 82 3.6585%
frameshift_deletion 0 0 0% 723 15977 4.5253%
frameshift_insertion 0 0 0% 543 13308 4.0803%
intergenic 2437568 15129055 16.1118% 176833 2238383 7.9%
intronic 3068879 17735594 17.3035% 238488 2641780 9.0275%
ncRNA_exonic 66243 400185 16.5531% 4572 54342 8.4134%
ncRNA_exonic;splicing 41 231 17.7489% 3 43 6.9767%
ncRNA_intronic 595396 3728327 15.9695% 45631 575920 7.9231%
ncRNA_splicing 391 2341 16.7023% 52 478 10.8787%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 404 8777 4.6029%
nonframeshift_insertion 0 0 0% 186 4784 3.888%
nonsynonymous 32453 336233 9.6519% 0 0 0%
splice_acceptor 54 750 7.2% 51 964 5.2905%
splice_donor 88 1076 8.1784% 21 763 2.7523%
splice_donor_acceptor 0 0 0% 15 45 33.3333%
splice_UTR5 50 400 12.5% 5 106 4.717%
splie_Others 0 0 0% 25 654 3.8226%
startloss 109 671 16.2444% 3 51 5.8824%
stopgain 369 4175 8.8383% 16 1252 1.278%
stoploss 48 353 13.5977% 2 63 3.1746%
synonymous 73561 548813 13.4037% 0 0 0%
upstream 124415 679592 18.3073% 9449 98760 9.5676%
upstream;downstream 10994 57451 19.1363% 906 9367 9.6723%
UTR3 55605 361040 15.4013% 5004 61415 8.1478%
UTR5 18193 112990 16.1014% 1317 16935 7.7768%
UTR5;UTR3 420 2524 16.6403% 45 381 11.811%
Total 6598512 39753026 16.5988% 493670 5848802 8.4405%
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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