Light Sussex
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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 Light Sussex
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region England
Purpose Dual
Description

The Sussex is a large breed that originated in the county of Sussex, England, and hence comes the name. It's a dual-purpose bird that was highly prized in its country of origin more than 100 years ago. The Sussex has made a huge contribution to the poultry industry and is even an ancestor to the modern Broiler chickens. Light Sussex have "silver" plumage which when crossed with a "gold" cockerel, such as a Rhode Island Red, will produce sex-linked chicks.

Characteristics

The Sussex has close fitted feathers, a single comb, red earlobes, and whitish-yellow legs. The Sussex has a wide, flat back, a deep breast and broad shoulders. Their tail is held at 45 degrees. Sussex hens are prolific layers of large tan to light-brown eggs (around 240 - 260 eggs per year). They occasionally go broody. On avarage, the weights for rooster and hen are 4.1 kg and 3.2 kg, respectively.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 98420 650455 15.1309% 9195 104154 8.8283%
exonic;splicing 27 188 14.3617% 0 0 0%
exonic_unknown 2 582 0.3436% 0 82 0%
frameshift_deletion 0 0 0% 535 15977 3.3486%
frameshift_insertion 0 0 0% 498 13308 3.7421%
intergenic 2276289 15129055 15.0458% 193281 2238383 8.6348%
intronic 2812896 17735594 15.8602% 248174 2641780 9.3942%
ncRNA_exonic 59302 400185 14.8186% 4568 54342 8.406%
ncRNA_exonic;splicing 44 231 19.0476% 3 43 6.9767%
ncRNA_intronic 568486 3728327 15.2478% 50738 575920 8.8099%
ncRNA_splicing 354 2341 15.1217% 53 478 11.0879%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 307 8777 3.4978%
nonframeshift_insertion 0 0 0% 148 4784 3.0936%
nonsynonymous 25641 336233 7.626% 0 0 0%
splice_acceptor 58 750 7.7333% 50 964 5.1867%
splice_donor 70 1076 6.5056% 14 763 1.8349%
splice_donor_acceptor 0 0 0% 12 45 26.6667%
splice_UTR5 48 400 12% 6 106 5.6604%
splie_Others 0 0 0% 20 654 3.0581%
startloss 75 671 11.1773% 5 51 9.8039%
stopgain 264 4175 6.3234% 12 1252 0.9585%
stoploss 59 353 16.7139% 4 63 6.3492%
synonymous 59427 548813 10.8283% 0 0 0%
upstream 102183 679592 15.0359% 8374 98760 8.4791%
upstream;downstream 8481 57451 14.7621% 762 9367 8.1349%
UTR3 49125 361040 13.6065% 5026 61415 8.1837%
UTR5 14306 112990 12.6613% 1066 16935 6.2947%
UTR5;UTR3 334 2524 13.233% 31 381 8.1365%
Total 6075891 39753026 15.2841% 522883 5848802 8.94%
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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