Background Information
| Breed Card | |
| Breed | Red Jungle Fowl |
| Species taxonomy | Gallus gallus spadiceus |
| Classification | Red Jungle Fowl |
| Region | Thailand |
| Purpose | Red Jungle Fowl |
The Red Jungle Fowl is a tropical bird in the family Phasianidae. It ranges across much of Southeast Asia and parts of South Asia. Red Jungle Fowl are the primary ancestor of the domestic chicken.Wild subspecies of Gallus gallus exist, including: G. g. gallus - from Southeast Asia; G. g. bankiva - from Java; G. g. jabouillei - from Vietnam and southern China; G. g. murghi - from India and Bangladesh; G. g. spadiceus - from Myanmar and southwestern China; G. g. philippensis - from Philippines.
Male Red Junglefowl are significantly larger than females. The male eclipse pattern includes a black feather in the middle of the back and small red-orange plumes spread across the body. Female eclipse plumage is generally indistinguishable from the plumage at other seasons, but the moulting schedule is the same as that of males. The Red Jungle Fowl has a much smaller body mass (around 2.25 lbs (1 kg) in females and 3.25 lbs (1.5kg) in males) and is brighter in coloration.
Variants Annotation&Density
| Annotation | Population SNP | Total SNP | Percentage SNP | Population INDEL | Total INDEL | Percentage INDEL |
|---|---|---|---|---|---|---|
| downstream | 173245 | 650455 | 26.6344% | 14110 | 104154 | 13.5472% |
| exonic;splicing | 30 | 188 | 15.9574% | 0 | 0 | 0% |
| exonic_unknown | 32 | 582 | 5.4983% | 1 | 82 | 1.2195% |
| frameshift_deletion | 0 | 0 | 0% | 486 | 15977 | 3.0419% |
| frameshift_insertion | 0 | 0 | 0% | 390 | 13308 | 2.9306% |
| intergenic | 4103088 | 15129055 | 27.1206% | 307873 | 2238383 | 13.7543% |
| intronic | 5140470 | 17735594 | 28.9839% | 412189 | 2641780 | 15.6027% |
| ncRNA_exonic | 106703 | 400185 | 26.6634% | 7519 | 54342 | 13.8364% |
| ncRNA_exonic;splicing | 76 | 231 | 32.9004% | 3 | 43 | 6.9767% |
| ncRNA_intronic | 1033884 | 3728327 | 27.7305% | 83631 | 575920 | 14.5213% |
| ncRNA_splicing | 634 | 2341 | 27.0824% | 69 | 478 | 14.4351% |
| ncRNA_UTR5 | 0 | 0 | 0% | 0 | 18 | 0% |
| nonframeshift_deletion | 0 | 0 | 0% | 329 | 8777 | 3.7484% |
| nonframeshift_insertion | 0 | 0 | 0% | 147 | 4784 | 3.0727% |
| nonsynonymous | 38175 | 336233 | 11.3537% | 0 | 0 | 0% |
| splice_acceptor | 97 | 750 | 12.9333% | 62 | 964 | 6.4315% |
| splice_donor | 129 | 1076 | 11.9888% | 32 | 763 | 4.194% |
| splice_donor_acceptor | 0 | 0 | 0% | 4 | 45 | 8.8889% |
| splice_UTR5 | 61 | 400 | 15.25% | 7 | 106 | 6.6038% |
| splie_Others | 0 | 0 | 0% | 33 | 654 | 5.0459% |
| startloss | 121 | 671 | 18.0328% | 2 | 51 | 3.9216% |
| stopgain | 390 | 4175 | 9.3413% | 22 | 1252 | 1.7572% |
| stoploss | 83 | 353 | 23.5127% | 6 | 63 | 9.5238% |
| synonymous | 101231 | 548813 | 18.4454% | 0 | 0 | 0% |
| upstream | 164032 | 679592 | 24.1368% | 11296 | 98760 | 11.4378% |
| upstream;downstream | 12289 | 57451 | 21.3904% | 896 | 9367 | 9.5655% |
| UTR3 | 86403 | 361040 | 23.9317% | 7690 | 61415 | 12.5214% |
| UTR5 | 19709 | 112990 | 17.4431% | 1136 | 16935 | 6.708% |
| UTR5;UTR3 | 498 | 2524 | 19.7306% | 43 | 381 | 11.2861% |
| Total | 10981380 | 39753026 | 27.624% | 847976 | 5848802 | 14.4983% |
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
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”.
