Lampung Kampung 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 Lampung Kampung chicken
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region Indonesia
Purpose Dual
Description

The Ayam Kampong (older spelling) or Ayam Kampung is a breed reported from Indonesia and Malaysia. The name means simply "free-range chicken" or literally "village chicken". In Indonesia, the term ayam kampung refer to indigenous chickens that are raised using traditional free range production techniques by almost every household in the village. It is a diverse population which resulted from the uncontrolled cross-breeding of red jungle-fowl, indigenous Southeast Asian chickens and exotic chickens of various types imported in the late 1800s by European, mainly Dutch and British settlers.

Characteristics

The Kampong is a small dual-purpose chicken. They are slow-growing breed that contributed to its low productivity. Both its physical characteristics and its colouring are highly variable. Three principal colour types are recognised. The commonest is the black-red variety, in which roosters are mainly green-black with glossy red-brown back, neck hackles and saddle feathers. Other varieties are the red type and the naked-neck type.The Kampong usually has red earlobes, which sometimes contain a blending of red and white. Also, their combs can be rose, pea, walnut or buttercup. Various color-verities are recognized for the Ayam Kampong, with the black-breasted red as the most common one.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 155834 650455 23.9577% 14010 104154 13.4512%
exonic;splicing 30 188 15.9574% 0 0 0%
exonic_unknown 3 582 0.5155% 0 82 0%
frameshift_deletion 0 0 0% 607 15977 3.7992%
frameshift_insertion 0 0 0% 550 13308 4.1329%
intergenic 3584075 15129055 23.69% 292395 2238383 13.0628%
intronic 4513735 17735594 25.4501% 390416 2641780 14.7785%
ncRNA_exonic 94412 400185 23.5921% 7302 54342 13.4371%
ncRNA_exonic;splicing 64 231 27.7056% 5 43 11.6279%
ncRNA_intronic 905967 3728327 24.2996% 78983 575920 13.7142%
ncRNA_splicing 553 2341 23.6224% 70 478 14.6444%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 382 8777 4.3523%
nonframeshift_insertion 0 0 0% 193 4784 4.0343%
nonsynonymous 38996 336233 11.5979% 0 0 0%
splice_acceptor 88 750 11.7333% 69 964 7.1577%
splice_donor 109 1076 10.1301% 25 763 3.2765%
splice_donor_acceptor 0 0 0% 12 45 26.6667%
splice_UTR5 64 400 16% 8 106 7.5472%
splie_Others 0 0 0% 38 654 5.8104%
startloss 130 671 19.3741% 4 51 7.8431%
stopgain 414 4175 9.9162% 16 1252 1.278%
stoploss 65 353 18.4136% 4 63 6.3492%
synonymous 91767 548813 16.721% 0 0 0%
upstream 154458 679592 22.728% 12049 98760 12.2003%
upstream;downstream 12390 57451 21.5662% 1032 9367 11.0174%
UTR3 78123 361040 21.6383% 7516 61415 12.2381%
UTR5 20972 112990 18.5609% 1489 16935 8.7924%
UTR5;UTR3 479 2524 18.9778% 44 381 11.5486%
Total 9652728 39753026 24.2817% 807220 5848802 13.8015%
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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