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Detailed information for vg1112762176:

Variant ID: vg1112762176 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12762176
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.02, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TGATAAAAGGAAATTATCATTATTATGGATCAATATAATTGTCAGATAAGAACACAGAAGGACTGCGAGTGTTCCATCTTTATGCAAACAAGGAATGTAA[G/T]
GACAAGCATCATCATGGTTTTCTCTTTCTTTTTAGTGATGCTAAGGGAGAATCATCTAGTATGTCTTCTTCATTGCCATCATCTTGCTCAACTTCAGTGC

Reverse complement sequence

GCACTGAAGTTGAGCAAGATGATGGCAATGAAGAAGACATACTAGATGATTCTCCCTTAGCATCACTAAAAAGAAAGAGAAAACCATGATGATGCTTGTC[C/A]
TTACATTCCTTGTTTGCATAAAGATGGAACACTCGCAGTCCTTCTGTGTTCTTATCTGACAATTATATTGATCCATAATAATGATAATTTCCTTTTATCA

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	40.30%	19.00%	0.97%	39.70%	NA
All Indica	2759	12.30%	22.60%	1.45%	63.65%	NA
All Japonica	1512	95.30%	0.40%	0.13%	4.17%	NA
Aus	269	1.10%	86.60%	1.49%	10.78%	NA
Indica I	595	11.80%	2.20%	2.18%	83.87%	NA
Indica II	465	3.20%	56.60%	0.65%	39.57%	NA
Indica III	913	15.90%	14.50%	1.64%	68.02%	NA
Indica Intermediate	786	13.90%	27.50%	1.15%	57.51%	NA
Temperate Japonica	767	96.60%	0.30%	0.13%	3.00%	NA
Tropical Japonica	504	92.10%	0.60%	0.20%	7.14%	NA
Japonica Intermediate	241	97.90%	0.40%	0.00%	1.66%	NA
VI/Aromatic	96	88.50%	9.40%	0.00%	2.08%	NA
Intermediate	90	42.20%	28.90%	0.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112762176	G -> T	LOC_Os11g22230.1	downstream_gene_variant ; 3876.0bp to feature; MODIFIER	silent_mutation	Average:13.031; most accessible tissue: Callus, score: 26.928	N	N	N	N
vg1112762176	G -> T	LOC_Os11g22240.1	intron_variant ; MODIFIER	silent_mutation	Average:13.031; most accessible tissue: Callus, score: 26.928	N	N	N	N
vg1112762176	G -> DEL	N	N	silent_mutation	Average:13.031; most accessible tissue: Callus, score: 26.928	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112762176	1.61E-06	1.05E-09	mr1277	Ind_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
vg1112762176	NA	6.75E-07	mr1609	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	1.08E-08	mr1675	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	2.97E-08	mr1806	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	2.10E-10	mr1829	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	2.32E-07	mr1842	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	3.75E-08	mr1902	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	2.01E-06	mr1062_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	3.32E-06	mr1154_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	1.52E-06	mr1158_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	2.89E-07	mr1167_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	4.22E-10	mr1829_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	5.24E-07	mr1842_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1112762176	NA	1.06E-09	mr1902_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251