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Detailed information for vg1116079879:

Variant ID: vg1116079879 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16079879
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

AGAAACAATAGCTTTAAATGGGATCAACATGCTCAAAGGGTTGTTTGGGATCTGTGTGACTTTCCTTGCTGGCCTTGGAACTCTTCAAATTCTTCTCCTG[C/T]
GAAAACGAACTCTCCGGAAACGTCGGAATCTAAACATAAAAGAGCAAAAACACCAAAACAGCACATAAACAAGCATGAACATACATGTGGATATTTTTAA

Reverse complement sequence

TTAAAAATATCCACATGTATGTTCATGCTTGTTTATGTGCTGTTTTGGTGTTTTTGCTCTTTTATGTTTAGATTCCGACGTTTCCGGAGAGTTCGTTTTC[G/A]
CAGGAGAAGAATTTGAAGAGTTCCAAGGCCAGCAAGGAAAGTCACACAGATCCCAAACAACCCTTTGAGCATGTTGATCCCATTTAAAGCTATTGTTTCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.70%	2.50%	18.13%	39.65%	NA
All Indica	2759	9.60%	4.30%	28.74%	57.34%	NA
All Japonica	1512	96.80%	0.00%	1.06%	2.12%	NA
Aus	269	6.30%	0.00%	13.38%	80.30%	NA
Indica I	595	14.80%	2.70%	25.04%	57.48%	NA
Indica II	465	9.50%	4.30%	25.59%	60.65%	NA
Indica III	913	4.90%	6.60%	32.20%	56.30%	NA
Indica Intermediate	786	11.30%	2.80%	29.39%	56.49%	NA
Temperate Japonica	767	96.90%	0.00%	1.83%	1.30%	NA
Tropical Japonica	504	96.20%	0.00%	0.40%	3.37%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	90.60%	0.00%	4.17%	5.21%	NA
Intermediate	90	46.70%	1.10%	8.89%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116079879	C -> T	LOC_Os11g27960.1	upstream_gene_variant ; 2308.0bp to feature; MODIFIER	silent_mutation	Average:9.728; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1116079879	C -> T	LOC_Os11g27940.1	downstream_gene_variant ; 4112.0bp to feature; MODIFIER	silent_mutation	Average:9.728; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1116079879	C -> T	LOC_Os11g27940-LOC_Os11g27960	intergenic_region ; MODIFIER	silent_mutation	Average:9.728; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1116079879	C -> DEL	N	N	silent_mutation	Average:9.728; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116079879	4.11E-06	9.05E-06	Yield	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652