Germany Commercial White Layer
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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 Germany Commercial White Layer
Species taxonomy Gallus gallus domesticus
Classification Commercial
Region Germany
Purpose Layer
Description

This is a commercial layer breed with white feather in Germany.

Characteristics

NA


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 62158 650455 9.5561% 5664 104154 5.4381%
exonic;splicing 15 188 7.9787% 0 0 0%
exonic_unknown 0 582 0% 0 82 0%
frameshift_deletion 0 0 0% 285 15977 1.7838%
frameshift_insertion 0 0 0% 262 13308 1.9687%
intergenic 1407448 15129055 9.3029% 118787 2238383 5.3068%
intronic 1789353 17735594 10.0891% 158349 2641780 5.994%
ncRNA_exonic 37260 400185 9.3107% 2918 54342 5.3697%
ncRNA_exonic;splicing 33 231 14.2857% 3 43 6.9767%
ncRNA_intronic 358225 3728327 9.6082% 32605 575920 5.6614%
ncRNA_splicing 218 2341 9.3123% 30 478 6.2762%
ncRNA_UTR5 0 0 0% 0 18 0%
nonframeshift_deletion 0 0 0% 161 8777 1.8343%
nonframeshift_insertion 0 0 0% 80 4784 1.6722%
nonsynonymous 15451 336233 4.5953% 0 0 0%
splice_acceptor 33 750 4.4% 33 964 3.4232%
splice_donor 32 1076 2.974% 9 763 1.1796%
splice_donor_acceptor 0 0 0% 4 45 8.8889%
splice_UTR5 29 400 7.25% 2 106 1.8868%
splie_Others 0 0 0% 18 654 2.7523%
startloss 63 671 9.389% 2 51 3.9216%
stopgain 158 4175 3.7844% 6 1252 0.4792%
stoploss 24 353 6.7989% 3 63 4.7619%
synonymous 36907 548813 6.7249% 0 0 0%
upstream 63743 679592 9.3796% 5064 98760 5.1276%
upstream;downstream 5444 57451 9.4759% 470 9367 5.0176%
UTR3 30750 361040 8.5171% 3160 61415 5.1453%
UTR5 9079 112990 8.0352% 667 16935 3.9386%
UTR5;UTR3 195 2524 7.7258% 21 381 5.5118%
Total 3816618 39753026 9.6008% 328603 5848802 5.6183%
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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