Ho
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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 Ho
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region Vietnam
Purpose Dual
Description

Ho chicken (Ga Hồ) originates from Ho village, Thuan Thanh district, Bac Ninh province, Vietnam. Ho is traditionally bred for fighting. Ho chickens have been raised in the household conditions of the rural area in Vietnam. Ho has been reported as endangered or critical breed in Vietnam.

Characteristics

Plumage, leg colors of Ho chickens were diverse. The roosters with walnut comb have the dark feather color while the hens with strawberry comb have the lighter one. Hens are poor layers (55 eggs per year). On avarage, the weights for rooster and hen are 3.78 kg and 2.64 kg, respectively.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 160167 650455 24.6238% 13879 104154 13.3255%
exonic;splicing 24 188 12.766% 0 0 0%
exonic_unknown 31 582 5.3265% 0 82 0%
frameshift_deletion 0 0 0% 503 15977 3.1483%
frameshift_insertion 0 0 0% 406 13308 3.0508%
intergenic 3919998 15129055 25.9104% 315844 2238383 14.1104%
intronic 4905454 17735594 27.6588% 419283 2641780 15.8712%
ncRNA_exonic 101959 400185 25.478% 7696 54342 14.1622%
ncRNA_exonic;splicing 67 231 29.0043% 5 43 11.6279%
ncRNA_intronic 1010453 3728327 27.102% 87366 575920 15.1698%
ncRNA_splicing 630 2341 26.9116% 75 478 15.6904%
ncRNA_UTR5 0 0 0% 0 18 0%
nonframeshift_deletion 0 0 0% 436 8777 4.9675%
nonframeshift_insertion 0 0 0% 140 4784 2.9264%
nonsynonymous 37552 336233 11.1684% 0 0 0%
splice_acceptor 97 750 12.9333% 61 964 6.3278%
splice_donor 112 1076 10.4089% 28 763 3.6697%
splice_donor_acceptor 0 0 0% 6 45 13.3333%
splice_UTR5 61 400 15.25% 8 106 7.5472%
splie_Others 0 0 0% 37 654 5.6575%
startloss 101 671 15.0522% 2 51 3.9216%
stopgain 351 4175 8.4072% 12 1252 0.9585%
stoploss 68 353 19.2635% 5 63 7.9365%
synonymous 90716 548813 16.5295% 0 0 0%
upstream 133073 679592 19.5813% 9898 98760 10.0223%
upstream;downstream 9157 57451 15.9388% 729 9367 7.7826%
UTR3 82912 361040 22.9648% 7908 61415 12.8763%
UTR5 15318 112990 13.557% 973 16935 5.7455%
UTR5;UTR3 412 2524 16.3233% 34 381 8.9239%
Total 10468713 39753026 26.3344% 865334 5848802 14.7951%
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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