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Detailed information for vg1125089739:

Variant ID: vg1125089739 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25089739
Reference Allele: G	Alternative Allele: T,C
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.79, G: 0.21, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

AAACGAACGGTCAAACATATTTAAAAAAGTCAACGGCGTCAAATATTTAGAAACGGAGGAAGTACTATAGTAGTTGTACCACACCTCTCCCTCTTGGCTC[G/T,C]
ACCACTTCCAAATTTCAATCCTATATACACACACACGAGAAATAAGACGATATTTGAGGTGAACAACATCCCAAAGTGTGGATGCTACTGGCAGGCATGG

Reverse complement sequence

CCATGCCTGCCAGTAGCATCCACACTTTGGGATGTTGTTCACCTCAAATATCGTCTTATTTCTCGTGTGTGTGTATATAGGATTGAAATTTGGAAGTGGT[C/A,G]
GAGCCAAGAGGGAGAGGTGTGGTACAACTACTATAGTACTTCCTCCGTTTCTAAATATTTGACGCCGTTGACTTTTTTAAATATGTTTGACCGTTCGTTT

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	47.80%	47.00%	0.59%	4.42%	C: 0.13%
All Indica	2759	41.00%	58.00%	0.65%	0.11%	C: 0.22%
All Japonica	1512	65.10%	21.10%	0.46%	13.29%	NA
Aus	269	17.80%	81.00%	0.00%	1.12%	NA
Indica I	595	29.70%	69.90%	0.34%	0.00%	NA
Indica II	465	58.70%	41.30%	0.00%	0.00%	NA
Indica III	913	30.60%	68.50%	0.33%	0.11%	C: 0.55%
Indica Intermediate	786	51.10%	46.80%	1.65%	0.25%	C: 0.13%
Temperate Japonica	767	68.60%	8.70%	0.91%	21.77%	NA
Tropical Japonica	504	58.70%	39.50%	0.00%	1.79%	NA
Japonica Intermediate	241	67.60%	22.00%	0.00%	10.37%	NA
VI/Aromatic	96	47.90%	51.00%	0.00%	1.04%	NA
Intermediate	90	56.70%	38.90%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125089739	G -> T	LOC_Os11g41760-LOC_Os11g41770	intergenic_region ; MODIFIER	silent_mutation	Average:54.42; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg1125089739	G -> DEL	N	N	silent_mutation	Average:54.42; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg1125089739	G -> C	LOC_Os11g41760-LOC_Os11g41770	intergenic_region ; MODIFIER	silent_mutation	Average:54.42; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125089739	NA	4.71E-06	mr1238	Jap_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
vg1125089739	NA	9.25E-06	mr1596	Jap_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
vg1125089739	NA	5.49E-09	mr1644	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
vg1125089739	NA	3.12E-11	mr1662	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
vg1125089739	NA	5.28E-06	mr1662	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
vg1125089739	NA	5.67E-16	mr1191_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
vg1125089739	NA	1.30E-10	mr1191_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
vg1125089739	4.75E-08	6.46E-14	mr1662_2	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
vg1125089739	4.96E-07	4.10E-09	mr1662_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
vg1125089739	NA	4.02E-07	mr1973_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