Old English Pheasant Fowl
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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 Old English Pheasant Fowl
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region England
Purpose Dual
Description

The Old English Pheasant Fowl is an extremely rare breed that originated in England. It is usually kept for egg production, but can also be used as a dual-purpose bird. English Pheasant Fowls are also related to Hamburgs and Derbyshire Redcaps, that share the same country of origin.

Characteristics

Old English Pheasant Fowls have rose combs, white earlobes and slate-blue legs. There are two color-varieties: gold and silver. English Pheasant hens lay plenty of white eggs (around 160 - 200 eggs per year) and they tend go broody too. The roosters weigh 2.7-3.2 kg; and the hens weigh 2.25-2.7 kg.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 98932 650455 15.2097% 9288 104154 8.9176%
exonic;splicing 22 188 11.7021% 0 0 0%
exonic_unknown 2 582 0.3436% 0 82 0%
frameshift_deletion 0 0 0% 527 15977 3.2985%
frameshift_insertion 0 0 0% 513 13308 3.8548%
intergenic 2268500 15129055 14.9943% 196276 2238383 8.7687%
intronic 2846889 17735594 16.0518% 255847 2641780 9.6846%
ncRNA_exonic 59674 400185 14.9116% 4758 54342 8.7557%
ncRNA_exonic;splicing 51 231 22.0779% 6 43 13.9535%
ncRNA_intronic 572896 3728327 15.366% 52534 575920 9.1218%
ncRNA_splicing 361 2341 15.4208% 49 478 10.251%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 291 8777 3.3155%
nonframeshift_insertion 0 0 0% 145 4784 3.0309%
nonsynonymous 25353 336233 7.5403% 0 0 0%
splice_acceptor 46 750 6.1333% 62 964 6.4315%
splice_donor 71 1076 6.5985% 18 763 2.3591%
splice_donor_acceptor 0 0 0% 20 45 44.4444%
splice_UTR5 50 400 12.5% 5 106 4.717%
splie_Others 0 0 0% 26 654 3.9755%
startloss 86 671 12.8167% 2 51 3.9216%
stopgain 261 4175 6.2515% 12 1252 0.9585%
stoploss 49 353 13.881% 3 63 4.7619%
synonymous 59710 548813 10.8798% 0 0 0%
upstream 102530 679592 15.087% 8376 98760 8.4812%
upstream;downstream 8401 57451 14.6229% 749 9367 7.9962%
UTR3 48974 361040 13.5647% 5167 61415 8.4133%
UTR5 14181 112990 12.5507% 1132 16935 6.6844%
UTR5;UTR3 324 2524 12.8368% 23 381 6.0367%
Total 6107363 39753026 15.3633% 535830 5848802 9.1614%
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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