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Detailed information for vg0229375522:

Variant ID: vg0229375522 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 29375522
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.02, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TACAAAACAAATGAATATTCTGCAGTGCCTTGTGATTCAGCATGTATACATTCCTTATATTTAACAAGAATCAGGGTTATGTGATCTAGTGGAAGCTTTC[T/A]
AGCAAATGCAGTGTTTTTCACTTAAATGACTTAAACTGGCAGGCAGTTTTCTTCATCAGCTGATGTTGGATAATTGCGGGTGAAGGGTAATAGAACGTGC

Reverse complement sequence

GCACGTTCTATTACCCTTCACCCGCAATTATCCAACATCAGCTGATGAAGAAAACTGCCTGCCAGTTTAAGTCATTTAAGTGAAAAACACTGCATTTGCT[A/T]
GAAAGCTTCCACTAGATCACATAACCCTGATTCTTGTTAAATATAAGGAATGTATACATGCTGAATCACAAGGCACTGCAGAATATTCATTTGTTTTGTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.00%	36.90%	0.08%	0.00%	NA
All Indica	2759	37.70%	62.20%	0.11%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	20.50%	79.20%	0.34%	0.00%	NA
Indica II	465	46.70%	53.30%	0.00%	0.00%	NA
Indica III	913	41.70%	58.20%	0.11%	0.00%	NA
Indica Intermediate	786	40.80%	59.20%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	77.80%	21.10%	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
vg0229375522	T -> A	LOC_Os02g48000.1	intron_variant ; MODIFIER	silent_mutation	Average:43.619; most accessible tissue: Callus, score: 70.269	N	N	N	N
vg0229375522	T -> A	LOC_Os02g48000.2	intron_variant ; MODIFIER	silent_mutation	Average:43.619; most accessible tissue: Callus, score: 70.269	N	N	N	N
vg0229375522	T -> A	LOC_Os02g48000.3	intron_variant ; MODIFIER	silent_mutation	Average:43.619; most accessible tissue: Callus, score: 70.269	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0229375522	NA	1.40E-06	mr1029	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
vg0229375522	NA	9.48E-06	mr1189	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
vg0229375522	NA	9.25E-07	mr1625	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
vg0229375522	NA	1.03E-08	mr1707	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
vg0229375522	NA	1.66E-06	mr1796	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
vg0229375522	3.24E-06	NA	mr1156_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
vg0229375522	8.20E-06	4.66E-06	mr1156_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
vg0229375522	NA	1.17E-08	mr1172_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
vg0229375522	9.98E-07	1.48E-16	mr1514_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
vg0229375522	8.53E-06	9.56E-06	mr1514_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