France Commercial Broiler
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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 France Commercial Broiler
Species taxonomy Gallus gallus domesticus
Classification Commercial
Region France
Purpose Broiler
Description

This is a commercial broiler breed of France.

Characteristics

NA


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 126414 650455 19.4347% 11319 104154 10.8676%
exonic;splicing 28 188 14.8936% 0 0 0%
exonic_unknown 0 582 0% 0 82 0%
frameshift_deletion 0 0 0% 482 15977 3.0168%
frameshift_insertion 0 0 0% 448 13308 3.3664%
intergenic 2859213 15129055 18.8988% 237948 2238383 10.6304%
intronic 3646594 17735594 20.5609% 317443 2641780 12.0163%
ncRNA_exonic 77060 400185 19.2561% 5882 54342 10.824%
ncRNA_exonic;splicing 57 231 24.6753% 5 43 11.6279%
ncRNA_intronic 743559 3728327 19.9435% 65781 575920 11.4219%
ncRNA_splicing 449 2341 19.1798% 55 478 11.5063%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 314 8777 3.5775%
nonframeshift_insertion 0 0 0% 143 4784 2.9891%
nonsynonymous 31190 336233 9.2763% 0 0 0%
splice_acceptor 70 750 9.3333% 59 964 6.1203%
splice_donor 94 1076 8.7361% 26 763 3.4076%
splice_donor_acceptor 0 0 0% 15 45 33.3333%
splice_UTR5 51 400 12.75% 6 106 5.6604%
splie_Others 0 0 0% 32 654 4.893%
startloss 115 671 17.1386% 2 51 3.9216%
stopgain 328 4175 7.8563% 16 1252 1.278%
stoploss 52 353 14.7309% 3 63 4.7619%
synonymous 74826 548813 13.6342% 0 0 0%
upstream 126870 679592 18.6686% 9726 98760 9.8481%
upstream;downstream 10252 57451 17.8448% 818 9367 8.7328%
UTR3 63506 361040 17.5897% 6189 61415 10.0773%
UTR5 17032 112990 15.0739% 1180 16935 6.9678%
UTR5;UTR3 402 2524 15.9271% 30 381 7.874%
Total 7778162 39753026 19.5662% 657923 5848802 11.2489%
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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