Merawang chicken
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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 Merawang chicken
Species taxonomy Gallus gallus domesticus
Classification Village
Region Indonesia
Purpose Unclear
Description

Merawang is a local breed of Indonesia.

Characteristics

Merawang hens produce in average of 165 eggs per-year that is much higher than other local hens which produce 40-60 eggs per-year.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 133843 650455 20.5768% 11117 104154 10.6736%
exonic;splicing 29 188 15.4255% 0 0 0%
exonic_unknown 5 582 0.8591% 0 82 0%
frameshift_deletion 0 0 0% 537 15977 3.3611%
frameshift_insertion 0 0 0% 446 13308 3.3514%
intergenic 3047795 15129055 20.1453% 232321 2238383 10.379%
intronic 3871233 17735594 21.8275% 314309 2641780 11.8976%
ncRNA_exonic 81383 400185 20.3363% 5905 54342 10.8664%
ncRNA_exonic;splicing 60 231 25.974% 3 43 6.9767%
ncRNA_intronic 771054 3728327 20.681% 63142 575920 10.9637%
ncRNA_splicing 477 2341 20.3759% 63 478 13.1799%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 346 8777 3.9421%
nonframeshift_insertion 0 0 0% 176 4784 3.6789%
nonsynonymous 34904 336233 10.3809% 0 0 0%
splice_acceptor 81 750 10.8% 64 964 6.639%
splice_donor 96 1076 8.9219% 22 763 2.8834%
splice_donor_acceptor 0 0 0% 12 45 26.6667%
splice_UTR5 64 400 16% 8 106 7.5472%
splie_Others 0 0 0% 32 654 4.893%
startloss 109 671 16.2444% 5 51 9.8039%
stopgain 364 4175 8.7186% 13 1252 1.0383%
stoploss 53 353 15.0142% 7 63 11.1111%
synonymous 82037 548813 14.9481% 0 0 0%
upstream 135654 679592 19.9611% 10092 98760 10.2187%
upstream;downstream 11134 57451 19.38% 840 9367 8.9677%
UTR3 67105 361040 18.5866% 6005 61415 9.7777%
UTR5 18629 112990 16.4873% 1212 16935 7.1568%
UTR5;UTR3 399 2524 15.8082% 34 381 8.9239%
Total 8256508 39753026 20.7695% 646712 5848802 11.0572%
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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