Luxi Game 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 Luxi Game chicken
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region China
Purpose Fighting
Description

Luxi Game chicken is a local breed ornamental type. The origin and mainly distribution area of Luxi Game chicken are Heze, Juancheng, Caoxian, Chengwu and other counties in southwest Shandong Province, China.

Characteristics

Luxi Game chickens are tall in body size. The heads are small. The faces are long and narrow. The beaks are yellow or jade. The combs are cushion type. The eyes are big and the eye sockets are deep. The earlobes are short and red. The skins are white and red when exposed. The shanks are yellow. The feathers are mainly black, red and white.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 157339 650455 24.1891% 13262 104154 12.7331%
exonic;splicing 32 188 17.0213% 0 0 0%
exonic_unknown 39 582 6.701% 0 82 0%
frameshift_deletion 0 0 0% 562 15977 3.5176%
frameshift_insertion 0 0 0% 472 13308 3.5467%
intergenic 3631309 15129055 24.0022% 279361 2238383 12.4805%
intronic 4541952 17735594 25.6092% 370205 2641780 14.0135%
ncRNA_exonic 95152 400185 23.777% 6839 54342 12.5851%
ncRNA_exonic;splicing 71 231 30.7359% 4 43 9.3023%
ncRNA_intronic 915627 3728327 24.5587% 75144 575920 13.0476%
ncRNA_splicing 566 2341 24.1777% 66 478 13.8075%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 372 8777 4.2384%
nonframeshift_insertion 0 0 0% 175 4784 3.658%
nonsynonymous 39317 336233 11.6934% 0 0 0%
splice_acceptor 84 750 11.2% 66 964 6.8465%
splice_donor 111 1076 10.316% 25 763 3.2765%
splice_donor_acceptor 0 0 0% 10 45 22.2222%
splice_UTR5 57 400 14.25% 9 106 8.4906%
splie_Others 0 0 0% 36 654 5.5046%
startloss 124 671 18.4799% 3 51 5.8824%
stopgain 379 4175 9.0778% 15 1252 1.1981%
stoploss 67 353 18.9802% 6 63 9.5238%
synonymous 93128 548813 16.969% 0 0 0%
upstream 151486 679592 22.2907% 10699 98760 10.8333%
upstream;downstream 12177 57451 21.1955% 937 9367 10.0032%
UTR3 79852 361040 22.1172% 7146 61415 11.6356%
UTR5 19516 112990 17.2723% 1200 16935 7.0859%
UTR5;UTR3 469 2524 18.5816% 35 381 9.1864%
Total 9738854 39753026 24.4984% 766650 5848802 13.1078%
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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