Modenese
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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 Modenese
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region Italy
Purpose Dual
Description

The Modenese has been described as a local breed by some authors. According to some others, the Modenese should be the result of crossbreeding among Padovana Comune (Improved Magiarola), White Livorno and Black Red Livorno. Because of the predominant black red variety wheaten, it was called Buff of Modena. The Modenese chicken appears in some paintings by Gaetano Chierici, an artist from Emilia-Romagna.

Characteristics

NA


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 118791 650455 18.2628% 11047 104154 10.6064%
exonic;splicing 23 188 12.234% 0 0 0%
exonic_unknown 17 582 2.921% 2 82 2.439%
frameshift_deletion 0 0 0% 708 15977 4.4314%
frameshift_insertion 0 0 0% 629 13308 4.7265%
intergenic 2717463 15129055 17.9619% 233346 2238383 10.4248%
intronic 3395526 17735594 19.1453% 303644 2641780 11.4939%
ncRNA_exonic 71469 400185 17.859% 5630 54342 10.3603%
ncRNA_exonic;splicing 43 231 18.6147% 4 43 9.3023%
ncRNA_intronic 677195 3728327 18.1635% 61696 575920 10.7126%
ncRNA_splicing 420 2341 17.9411% 53 478 11.0879%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 404 8777 4.6029%
nonframeshift_insertion 0 0 0% 186 4784 3.888%
nonsynonymous 31490 336233 9.3655% 0 0 0%
splice_acceptor 63 750 8.4% 64 964 6.639%
splice_donor 84 1076 7.8067% 22 763 2.8834%
splice_donor_acceptor 0 0 0% 18 45 40%
splice_UTR5 56 400 14% 6 106 5.6604%
splie_Others 0 0 0% 38 654 5.8104%
startloss 109 671 16.2444% 2 51 3.9216%
stopgain 336 4175 8.0479% 17 1252 1.3578%
stoploss 63 353 17.847% 3 63 4.7619%
synonymous 73424 548813 13.3787% 0 0 0%
upstream 123156 679592 18.122% 10018 98760 10.1438%
upstream;downstream 10138 57451 17.6463% 900 9367 9.6082%
UTR3 58804 361040 16.2874% 6158 61415 10.0269%
UTR5 17101 112990 15.135% 1366 16935 8.0661%
UTR5;UTR3 399 2524 15.8082% 36 381 9.4488%
Total 7296170 39753026 18.3537% 635998 5848802 10.874%
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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