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Detailed information for vg0316526266:

Variant ID: vg0316526266 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16526266
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.10, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

CAGGGACAACGAAGACTGGATCTGAATCTTCTATTTGAAGATAGAACCATCTCGCCCGCCATTTACTGCAAGAAGAGGGGCACTGGAAGGGGATGTATCA[T/C]
GACTTCAGGCCATCCCAAAGTCGGAAACCAACACACCCGGATACCTTTTTAGGTTCCATCCAGAGCAACTCGTAATAGAAACGAAACAGGTCAAGAAACG

Reverse complement sequence

CGTTTCTTGACCTGTTTCGTTTCTATTACGAGTTGCTCTGGATGGAACCTAAAAAGGTATCCGGGTGTGTTGGTTTCCGACTTTGGGATGGCCTGAAGTC[A/G]
TGATACATCCCCTTCCAGTGCCCCTCTTCTTGCAGTAAATGGCGGGCGAGATGGTTCTATCTTCAAATAGAAGATTCAGATCCAGTCTTCGTTGTCCCTG

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	58.30%	29.10%	0.85%	11.85%	NA
All Indica	2759	71.50%	23.50%	0.14%	4.89%	NA
All Japonica	1512	35.70%	38.60%	1.98%	23.68%	NA
Aus	269	66.20%	11.90%	1.49%	20.45%	NA
Indica I	595	58.30%	41.50%	0.17%	0.00%	NA
Indica II	465	90.50%	7.50%	0.22%	1.72%	NA
Indica III	913	71.00%	22.10%	0.00%	6.90%	NA
Indica Intermediate	786	70.90%	20.70%	0.25%	8.14%	NA
Temperate Japonica	767	11.20%	48.50%	3.39%	36.90%	NA
Tropical Japonica	504	66.50%	25.60%	0.00%	7.94%	NA
Japonica Intermediate	241	49.40%	34.40%	1.66%	14.52%	NA
VI/Aromatic	96	9.40%	86.50%	1.04%	3.12%	NA
Intermediate	90	58.90%	30.00%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0316526266	T -> C	LOC_Os03g29085.1	downstream_gene_variant ; 3285.0bp to feature; MODIFIER	silent_mutation	Average:58.222; most accessible tissue: Minghui63 flag leaf, score: 72.907	N	N	N	N
vg0316526266	T -> C	LOC_Os03g29100.1	intron_variant ; MODIFIER	silent_mutation	Average:58.222; most accessible tissue: Minghui63 flag leaf, score: 72.907	N	N	N	N
vg0316526266	T -> DEL	N	N	silent_mutation	Average:58.222; most accessible tissue: Minghui63 flag leaf, score: 72.907	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316526266	NA	3.55E-07	mr1045_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
vg0316526266	NA	3.14E-06	mr1318_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
vg0316526266	NA	7.60E-06	mr1381_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
vg0316526266	6.30E-07	6.28E-07	mr1387_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
vg0316526266	1.39E-06	1.39E-06	mr1432_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
vg0316526266	NA	3.60E-06	mr1456_2	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
vg0316526266	2.81E-06	2.81E-06	mr1459_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
vg0316526266	NA	2.85E-06	mr1465_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
vg0316526266	7.31E-06	7.31E-06	mr1719_2	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
vg0316526266	NA	9.28E-06	mr1729_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
vg0316526266	NA	5.84E-07	mr1736_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
vg0316526266	NA	3.16E-06	mr1740_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
vg0316526266	NA	2.19E-06	mr1785_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
vg0316526266	NA	1.88E-07	mr1804_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
vg0316526266	NA	9.48E-06	mr1849_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
vg0316526266	NA	1.16E-06	mr1887_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
vg0316526266	NA	3.00E-06	mr1968_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