Sumatra 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 Sumatra chicken
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region Indonesia
Purpose Fancy
Description

The Sumatra is a breed native to the island of Sumatra in Indonesia. The birds originally imported to Europe for cockfighting, but now they are almost a purely exhibition breed. In 1883, the Black Sumatra was accepted into the American Standard of Perfection. They were brought into Britain in 1902 by Frederick R Eaton of Norwich. They are on the critical list and breeders all over the world but mainly in the UK and America are doing all they can to save the breed from extinction.

Characteristics

Sumatras sport pea combs, red or reddish-black wattles and earlobes (almost all black in hens), and slate-dark legs and feet. Sumatras have attractive plumage colors including; blue, white, splash and black. Both roosters and hens have long Pheasant-like tail feathers, with the males' saddle feathers almost touching the ground. Sumatras are also described as excellent flyers. Sumatra hens are poor layers with yearly totals of almost 100 white eggs, and are exceptionally susceptible to broodiness. The roosters weigh 2.25 - 2.7 kg; and the hens usually weigh 1.8 kg.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 165005 650455 25.3676% 14331 104154 13.7594%
exonic;splicing 34 188 18.0851% 0 0 0%
exonic_unknown 20 582 3.4364% 0 82 0%
frameshift_deletion 0 0 0% 754 15977 4.7193%
frameshift_insertion 0 0 0% 613 13308 4.6063%
intergenic 3720286 15129055 24.5903% 298546 2238383 13.3376%
intronic 4681151 17735594 26.3941% 397181 2641780 15.0346%
ncRNA_exonic 98543 400185 24.6244% 7299 54342 13.4316%
ncRNA_exonic;splicing 67 231 29.0043% 4 43 9.3023%
ncRNA_intronic 933681 3728327 25.0429% 79864 575920 13.8672%
ncRNA_splicing 559 2341 23.8787% 75 478 15.6904%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 471 8777 5.3663%
nonframeshift_insertion 0 0 0% 202 4784 4.2224%
nonsynonymous 43420 336233 12.9137% 0 0 0%
splice_acceptor 94 750 12.5333% 72 964 7.4689%
splice_donor 128 1076 11.8959% 28 763 3.6697%
splice_donor_acceptor 0 0 0% 12 45 26.6667%
splice_UTR5 76 400 19% 8 106 7.5472%
splie_Others 0 0 0% 42 654 6.422%
startloss 128 671 19.076% 3 51 5.8824%
stopgain 480 4175 11.497% 18 1252 1.4377%
stoploss 86 353 24.3626% 6 63 9.5238%
synonymous 100401 548813 18.2942% 0 0 0%
upstream 167587 679592 24.6599% 12857 98760 13.0184%
upstream;downstream 13908 57451 24.2085% 1108 9367 11.8288%
UTR3 83442 361040 23.1116% 7957 61415 12.9561%
UTR5 22981 112990 20.339% 1608 16935 9.4951%
UTR5;UTR3 537 2524 21.2758% 48 381 12.5984%
Total 10032614 39753026 25.2374% 823108 5848802 14.0731%
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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