Ancona
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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 Ancona
Species taxonomy Gallus gallus domesticus
Classification Commercial
Region Italy
Purpose Layer
Description

The Ancona is a breed of chicken which originated in the Marche region of Italy. This breed is named after the city of Ancona, capital of the Marche. It was bred to its present type mainly in United Kingdom during 19th Century. It is popular in Britain and the United States, but uncommon in Italy. An initiative to re-establish it in and preserve its biodiversity in Italy was launched in 2000. There are also Ancona bantams.

Characteristics

The Ancona is a good layer of white eggs, of which it lays an average of 220 per year. Hens have little tendency to broodiness. Pullets may begin to lay at 5 months. Birds range widely and take flight easily. The plumage of the Ancona is black mottled with white. Approximately one feather in three has a v-shaped white marking at the tip. All primaries, sickles and tail-feathers should have white tips. The black feathers may have a beetle-green tint. In Italy, blue mottled with white is also recognised in full-size birds, but not in bantams. Australia recognises a Red variety, with a chestnut to red bay ground colour. The legs are yellow mottled with black, the beak yellow with some black markings on the upper mandible, and the eye orange-red. The skin is yellow, the ear-lobes white or cream-coloured. The comb is of medium size, with five well-marked points; in hens it should fall gracefully to one side. In the United Kingdom and in the United States, but not in Italy, a rose comb is permitted.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 122373 650455 18.8134% 11122 104154 10.6784%
exonic;splicing 22 188 11.7021% 0 0 0%
exonic_unknown 21 582 3.6082% 1 82 1.2195%
frameshift_deletion 0 0 0% 614 15977 3.843%
frameshift_insertion 0 0 0% 526 13308 3.9525%
intergenic 2810073 15129055 18.574% 237225 2238383 10.5981%
intronic 3518746 17735594 19.84% 309314 2641780 11.7085%
ncRNA_exonic 73728 400185 18.4235% 5710 54342 10.5075%
ncRNA_exonic;splicing 52 231 22.5108% 4 43 9.3023%
ncRNA_intronic 713779 3728327 19.1448% 64088 575920 11.1279%
ncRNA_splicing 461 2341 19.6924% 58 478 12.1339%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 361 8777 4.113%
nonframeshift_insertion 0 0 0% 167 4784 3.4908%
nonsynonymous 31704 336233 9.4292% 0 0 0%
splice_acceptor 66 750 8.8% 57 964 5.9129%
splice_donor 91 1076 8.4572% 22 763 2.8834%
splice_donor_acceptor 0 0 0% 13 45 28.8889%
splice_UTR5 58 400 14.5% 8 106 7.5472%
splie_Others 0 0 0% 31 654 4.7401%
startloss 99 671 14.7541% 5 51 9.8039%
stopgain 347 4175 8.3114% 23 1252 1.8371%
stoploss 54 353 15.2975% 5 63 7.9365%
synonymous 74773 548813 13.6245% 0 0 0%
upstream 123906 679592 18.2324% 9651 98760 9.7722%
upstream;downstream 10041 57451 17.4775% 802 9367 8.562%
UTR3 60617 361040 16.7896% 6172 61415 10.0497%
UTR5 16830 112990 14.8951% 1152 16935 6.8025%
UTR5;UTR3 388 2524 15.3724% 36 381 9.4488%
Total 7558229 39753026 19.013% 647168 5848802 11.065%
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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