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

Yanjin Black-bone chickens are a local breed of Yunnan province. It has a long breeding history. The origin and mainly disstribution area of Yanjin Black-bone chickens are Yanjin, Yiliang, Suijiang, Daguan and Yongshan counties of Yunnan, China.

Characteristics

Yanjin Black-bone chicken is a local breed used for both meat and egg. Yanjin Black-bone chicken is large in size. The beaks are long with slightly curved, dark in color. The comb is single comb and in black or red color. The wattles, earlobes, eyes and faces are black. The color of feathers are black, gray, black-yellow, yellow, white or red. The skins are black. Most individuals have no shank feathers, the shank and toes are black.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 170869 650455 26.2692% 15452 104154 14.8357%
exonic;splicing 34 188 18.0851% 0 0 0%
exonic_unknown 40 582 6.8729% 0 82 0%
frameshift_deletion 0 0 0% 879 15977 5.5017%
frameshift_insertion 0 0 0% 736 13308 5.5305%
intergenic 3902261 15129055 25.7932% 316484 2238383 14.139%
intronic 4872705 17735594 27.4742% 417564 2641780 15.8062%
ncRNA_exonic 102197 400185 25.5374% 7632 54342 14.0444%
ncRNA_exonic;splicing 76 231 32.9004% 4 43 9.3023%
ncRNA_intronic 977060 3728327 26.2064% 84208 575920 14.6215%
ncRNA_splicing 616 2341 26.3135% 66 478 13.8075%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 493 8777 5.617%
nonframeshift_insertion 0 0 0% 251 4784 5.2467%
nonsynonymous 45862 336233 13.6399% 0 0 0%
splice_acceptor 100 750 13.3333% 84 964 8.7137%
splice_donor 144 1076 13.3829% 29 763 3.8008%
splice_donor_acceptor 0 0 0% 14 45 31.1111%
splice_UTR5 75 400 18.75% 8 106 7.5472%
splie_Others 0 0 0% 40 654 6.1162%
startloss 144 671 21.4605% 5 51 9.8039%
stopgain 471 4175 11.2814% 19 1252 1.5176%
stoploss 73 353 20.6799% 6 63 9.5238%
synonymous 103424 548813 18.845% 0 0 0%
upstream 176529 679592 25.9757% 14018 98760 14.194%
upstream;downstream 14878 57451 25.8969% 1262 9367 13.4728%
UTR3 85599 361040 23.709% 8205 61415 13.3599%
UTR5 25043 112990 22.1639% 1911 16935 11.2843%
UTR5;UTR3 573 2524 22.7021% 58 381 15.2231%
Total 10478773 39753026 26.3597% 869429 5848802 14.8651%
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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