Brahma
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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 Brahma
Species taxonomy Gallus gallus domesticus
Classification Commercial
Region America
Purpose Broiler
Description

The Brahma is a large breed of chicken developed in the United States from birds imported from Shanghai of China. The Brahma was the principal broiler breed in the United States from the 1850s until about 1930. It is also a good layer of large brown eggs, which weigh approximately 55-60 g.

Characteristics

"The Brahma has pea comb; medium-zise, well-rounded wattles; large and long earlobes. All are red. The chicken has yellow beak; reddish brown eyes; yellow shanks and toes. As for the variaty of Dark Brahma chicken, it fits the description for standard silver penciled plumage. The rooster's shank and outer toe feathers are black. The hen's shank feathers are penciled with steel gray."


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 133933 650455 20.5907% 12285 104154 11.795%
exonic;splicing 34 188 18.0851% 0 0 0%
exonic_unknown 25 582 4.2955% 0 82 0%
frameshift_deletion 0 0 0% 713 15977 4.4627%
frameshift_insertion 0 0 0% 605 13308 4.5461%
intergenic 3071887 15129055 20.3046% 254566 2238383 11.3728%
intronic 3836908 17735594 21.6339% 333427 2641780 12.6213%
ncRNA_exonic 80154 400185 20.0292% 6109 54342 11.2418%
ncRNA_exonic;splicing 60 231 25.974% 1 43 2.3256%
ncRNA_intronic 774052 3728327 20.7614% 67700 575920 11.7551%
ncRNA_splicing 468 2341 19.9915% 59 478 12.3431%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 422 8777 4.808%
nonframeshift_insertion 0 0 0% 190 4784 3.9716%
nonsynonymous 34701 336233 10.3205% 0 0 0%
splice_acceptor 74 750 9.8667% 69 964 7.1577%
splice_donor 87 1076 8.0855% 26 763 3.4076%
splice_donor_acceptor 0 0 0% 11 45 24.4444%
splice_UTR5 65 400 16.25% 7 106 6.6038%
splie_Others 0 0 0% 46 654 7.0336%
startloss 118 671 17.5857% 5 51 9.8039%
stopgain 388 4175 9.2934% 20 1252 1.5974%
stoploss 64 353 18.1303% 6 63 9.5238%
synonymous 81078 548813 14.7733% 0 0 0%
upstream 138690 679592 20.4078% 11125 98760 11.2647%
upstream;downstream 11379 57451 19.8064% 987 9367 10.537%
UTR3 66504 361040 18.4201% 6857 61415 11.165%
UTR5 19235 112990 17.0236% 1463 16935 8.6389%
UTR5;UTR3 439 2524 17.393% 38 381 9.9738%
Total 8250343 39753026 20.754% 696738 5848802 11.9125%
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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