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Detailed information for vg1124646669:

Variant ID: vg1124646669 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24646669
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, T: 0.08, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TGCGCCTTCCTGTATATAACTCTCCAGAGGAGCGATGCCCTTTGTGATGTACCGTGTACTGTTTTTGCCTATGCTCTTTTCCCCCCCATTTTCTCCTTCA[T/G]
TCTGATCAGGAAACAAACCATGACAACGCTGGCATTGTTGCCCTTTTCGCCTTGTTCATTTGAGCTTTCTTGTTAGACTTTGTGGGATAACCATATATTT

Reverse complement sequence

AAATATATGGTTATCCCACAAAGTCTAACAAGAAAGCTCAAATGAACAAGGCGAAAAGGGCAACAATGCCAGCGTTGTCATGGTTTGTTTCCTGATCAGA[A/C]
TGAAGGAGAAAATGGGGGGGAAAAGAGCATAGGCAAAAACAGTACACGGTACATCACAAAGGGCATCGCTCCTCTGGAGAGTTATATACAGGAAGGCGCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.20%	22.70%	0.08%	0.00%	NA
All Indica	2759	97.20%	2.80%	0.00%	0.00%	NA
All Japonica	1512	45.20%	54.60%	0.20%	0.00%	NA
Aus	269	62.10%	37.90%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	95.20%	4.80%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	3.10%	0.00%	0.00%	NA
Temperate Japonica	767	29.20%	70.80%	0.00%	0.00%	NA
Tropical Japonica	504	65.30%	34.50%	0.20%	0.00%	NA
Japonica Intermediate	241	53.90%	45.20%	0.83%	0.00%	NA
VI/Aromatic	96	49.00%	51.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	22.20%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124646669	T -> G	LOC_Os11g41130.2	3_prime_UTR_variant ; 186.0bp to feature; MODIFIER	silent_mutation	Average:76.589; most accessible tissue: Zhenshan97 root, score: 81.772	N	N	N	N
vg1124646669	T -> G	LOC_Os11g41140.1	upstream_gene_variant ; 1378.0bp to feature; MODIFIER	silent_mutation	Average:76.589; most accessible tissue: Zhenshan97 root, score: 81.772	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124646669	NA	9.44E-06	mr1112_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251