Xichuan Black-bone chicken
Jump to
section
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 Xichuan Black-bone chicken
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region China
Purpose Dual
Description

Xichuan Black-bone chickens are a local breed used for meat and eggs. They originated and distributed in Xichuan County, Henan Province, China.

Characteristics

Xichuan black-bone chickens are small in body size.They have white, yellow and black feathers. They are characterized with "black skin, black meat and black bone". The beaks are black. They have single comb. The skins are white or gray. The shanks are black. The hens start laying at 160-180 days and lay 145-155 eggs a year.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 155489 650455 23.9047% 14343 104154 13.771%
exonic;splicing 30 188 15.9574% 0 0 0%
exonic_unknown 35 582 6.0137% 0 82 0%
frameshift_deletion 0 0 0% 823 15977 5.1512%
frameshift_insertion 0 0 0% 715 13308 5.3727%
intergenic 3538468 15129055 23.3886% 292104 2238383 13.0498%
intronic 4430814 17735594 24.9826% 383727 2641780 14.5253%
ncRNA_exonic 92948 400185 23.2263% 7055 54342 12.9826%
ncRNA_exonic;splicing 64 231 27.7056% 5 43 11.6279%
ncRNA_intronic 894435 3728327 23.9903% 78406 575920 13.614%
ncRNA_splicing 561 2341 23.9641% 72 478 15.0628%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 481 8777 5.4802%
nonframeshift_insertion 0 0 0% 223 4784 4.6614%
nonsynonymous 41031 336233 12.2031% 0 0 0%
splice_acceptor 82 750 10.9333% 78 964 8.0913%
splice_donor 114 1076 10.5948% 25 763 3.2765%
splice_donor_acceptor 0 0 0% 23 45 51.1111%
splice_UTR5 72 400 18% 10 106 9.434%
splie_Others 0 0 0% 31 654 4.7401%
startloss 133 671 19.8212% 8 51 15.6863%
stopgain 417 4175 9.988% 23 1252 1.8371%
stoploss 72 353 20.3966% 8 63 12.6984%
synonymous 93478 548813 17.0328% 0 0 0%
upstream 160602 679592 23.6321% 12935 98760 13.0974%
upstream;downstream 13538 57451 23.5644% 1195 9367 12.7576%
UTR3 77466 361040 21.4563% 7535 61415 12.269%
UTR5 22569 112990 19.9743% 1732 16935 10.2273%
UTR5;UTR3 503 2524 19.9287% 48 381 12.5984%
Total 9522921 39753026 23.9552% 801606 5848802 13.7055%
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”.

0.409678s