Penedesenca
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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 Penedesenca
Species taxonomy Gallus gallus domesticus
Classification Commercial
Region Spain
Purpose Layer
Description

The Penedesenca is a breed of chicken originating in the Spanish region of Catalonia, in the area around Vilafranca del Penedes, the main town of the historical Penedes region. It was developed in the first half of the 20th century from native barnyard chickens. Penedesencas are noted for their dark brown eggs, which are among the darkest eggs in the poultry world.

Characteristics

Penedesencas have red earlobes with a white center, and unusual combs called the king's comb or the carnation comb. Their comb is similar to the common single comb, but with several lobes at the rear. The original leg color is slate-dark, but brighter colors are common in the newly developed color-varieties. Penedesenca hens lay around 140 - 160 eggs per year, but they don't usually go broody. The roosters weigh 2 - 3 kg; and the hens weigh 1.7 - 2.4 kg.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 66916 650455 10.2876% 6566 104154 6.3041%
exonic;splicing 15 188 7.9787% 0 0 0%
exonic_unknown 1 582 0.1718% 0 82 0%
frameshift_deletion 0 0 0% 362 15977 2.2658%
frameshift_insertion 0 0 0% 356 13308 2.6751%
intergenic 1516724 15129055 10.0252% 132650 2238383 5.9262%
intronic 1933526 17735594 10.902% 175580 2641780 6.6463%
ncRNA_exonic 39992 400185 9.9934% 3272 54342 6.0211%
ncRNA_exonic;splicing 33 231 14.2857% 4 43 9.3023%
ncRNA_intronic 376234 3728327 10.0912% 34947 575920 6.068%
ncRNA_splicing 257 2341 10.9782% 33 478 6.9038%
ncRNA_UTR5 0 0 0% 0 18 0%
nonframeshift_deletion 0 0 0% 199 8777 2.2673%
nonframeshift_insertion 0 0 0% 96 4784 2.0067%
nonsynonymous 17111 336233 5.089% 0 0 0%
splice_acceptor 41 750 5.4667% 39 964 4.0456%
splice_donor 41 1076 3.8104% 18 763 2.3591%
splice_donor_acceptor 0 0 0% 8 45 17.7778%
splice_UTR5 26 400 6.5% 4 106 3.7736%
splie_Others 0 0 0% 21 654 3.211%
startloss 62 671 9.2399% 2 51 3.9216%
stopgain 182 4175 4.3593% 10 1252 0.7987%
stoploss 31 353 8.7819% 5 63 7.9365%
synonymous 40080 548813 7.303% 0 0 0%
upstream 68682 679592 10.1064% 5715 98760 5.7868%
upstream;downstream 5720 57451 9.9563% 471 9367 5.0283%
UTR3 32809 361040 9.0874% 3484 61415 5.6729%
UTR5 9501 112990 8.4087% 730 16935 4.3106%
UTR5;UTR3 247 2524 9.7861% 29 381 7.6115%
Total 4108231 39753026 10.3344% 364601 5848802 6.2338%
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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