Hubei black-silkies
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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 Hubei black-silkies
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region China
Purpose Dual
Description

This breed is a traditional black-bone chicken breed of Hubei province, China. The feather of this breed chicken is black.

Characteristics

NA


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 175043 650455 26.9109% 16193 104154 15.5472%
exonic;splicing 38 188 20.2128% 0 0 0%
exonic_unknown 11 582 1.89% 0 82 0%
frameshift_deletion 0 0 0% 940 15977 5.8835%
frameshift_insertion 0 0 0% 806 13308 6.0565%
intergenic 4024809 15129055 26.6032% 337618 2238383 15.0831%
intronic 4987676 17735594 28.1224% 439054 2641780 16.6196%
ncRNA_exonic 105730 400185 26.4203% 8225 54342 15.1356%
ncRNA_exonic;splicing 75 231 32.4675% 4 43 9.3023%
ncRNA_intronic 1011796 3728327 27.1381% 89866 575920 15.6039%
ncRNA_splicing 585 2341 24.9893% 74 478 15.4812%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 592 8777 6.7449%
nonframeshift_insertion 0 0 0% 281 4784 5.8737%
nonsynonymous 48304 336233 14.3662% 0 0 0%
splice_acceptor 106 750 14.1333% 97 964 10.0622%
splice_donor 128 1076 11.8959% 33 763 4.325%
splice_donor_acceptor 0 0 0% 19 45 42.2222%
splice_UTR5 87 400 21.75% 9 106 8.4906%
splie_Others 0 0 0% 37 654 5.6575%
startloss 153 671 22.8018% 5 51 9.8039%
stopgain 536 4175 12.8383% 24 1252 1.9169%
stoploss 84 353 23.796% 8 63 12.6984%
synonymous 106277 548813 19.3649% 0 0 0%
upstream 180971 679592 26.6294% 14753 98760 14.9382%
upstream;downstream 15257 57451 26.5565% 1326 9367 14.1561%
UTR3 88889 361040 24.6203% 8859 61415 14.4248%
UTR5 26082 112990 23.0835% 2101 16935 12.4063%
UTR5;UTR3 613 2524 24.2868% 60 381 15.748%
Total 10773250 39753026 27.1005% 920985 5848802 15.7466%
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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