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Detailed information for vg0235815991:

Variant ID: vg0235815991 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 35815991
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCGTGGCAATTACAATGCAGCATGATTCCATGCATAACTTTCACAGGTGATATCGACTGAGTGGGTTTTGGCACCAACTTAGGAGTTAGAAAAAACAA[T/G]
AACAGACCAAAAAAAATCTGGATTCTGAAAATAAAGGAATGAAGGCACAAAGCATACTTCAGGATAGATTCAACTGTCCTTTGCAAATAGTCTGGTCGAT

Reverse complement sequence

ATCGACCAGACTATTTGCAAAGGACAGTTGAATCTATCCTGAAGTATGCTTTGTGCCTTCATTCCTTTATTTTCAGAATCCAGATTTTTTTTGGTCTGTT[A/C]
TTGTTTTTTCTAACTCCTAAGTTGGTGCCAAAACCCACTCAGTCGATATCACCTGTGAAAGTTATGCATGGAATCATGCTGCATTGTAATTGCCACGCTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.50%	1.80%	0.66%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	92.50%	5.60%	1.92%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	85.30%	11.00%	3.78%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	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
vg0235815991	T -> G	LOC_Os02g58600.1	upstream_gene_variant ; 3117.0bp to feature; MODIFIER	silent_mutation	Average:49.323; most accessible tissue: Callus, score: 74.217	N	N	N	N
vg0235815991	T -> G	LOC_Os02g58580.1	downstream_gene_variant ; 3545.0bp to feature; MODIFIER	silent_mutation	Average:49.323; most accessible tissue: Callus, score: 74.217	N	N	N	N
vg0235815991	T -> G	LOC_Os02g58580.2	downstream_gene_variant ; 3545.0bp to feature; MODIFIER	silent_mutation	Average:49.323; most accessible tissue: Callus, score: 74.217	N	N	N	N
vg0235815991	T -> G	LOC_Os02g58580.4	downstream_gene_variant ; 3545.0bp to feature; MODIFIER	silent_mutation	Average:49.323; most accessible tissue: Callus, score: 74.217	N	N	N	N
vg0235815991	T -> G	LOC_Os02g58580.5	downstream_gene_variant ; 3545.0bp to feature; MODIFIER	silent_mutation	Average:49.323; most accessible tissue: Callus, score: 74.217	N	N	N	N
vg0235815991	T -> G	LOC_Os02g58590.1	intron_variant ; MODIFIER	silent_mutation	Average:49.323; most accessible tissue: Callus, score: 74.217	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0235815991	NA	9.98E-08	mr1210	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
vg0235815991	9.63E-06	6.69E-08	mr1305	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
vg0235815991	4.73E-06	4.73E-06	mr1409	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
vg0235815991	NA	1.91E-09	mr1585	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
vg0235815991	NA	1.51E-07	mr1586	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
vg0235815991	NA	8.46E-07	mr1765	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
vg0235815991	2.76E-08	1.98E-10	mr1305_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
vg0235815991	3.25E-06	3.75E-09	mr1585_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