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Detailed information for vg0329897160:

Variant ID: vg0329897160 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 29897160
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.78, T: 0.23, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

AGAATGTGGTACCTAACTACAATAGCAAAGCCAAATTAGAACTTAGAATTTACGAGTAAGAAAATGTAGAAGATTGTTGAAAAAGGAACAGCGGGATAGC[A/T]
TGAAACTGGCATCATACCAATCCTATAAATGTGAGATTTGCCTCATCATCATAGCTAAGGCTTTGTTGACCTTCTGGCATTCGTTTTAATGCTAATGCTA

Reverse complement sequence

TAGCATTAGCATTAAAACGAATGCCAGAAGGTCAACAAAGCCTTAGCTATGATGATGAGGCAAATCTCACATTTATAGGATTGGTATGATGCCAGTTTCA[T/A]
GCTATCCCGCTGTTCCTTTTTCAACAATCTTCTACATTTTCTTACTCGTAAATTCTAAGTTCTAATTTGGCTTTGCTATTGTAGTTAGGTACCACATTCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.00%	49.80%	0.15%	0.08%	NA
All Indica	2759	26.00%	73.60%	0.25%	0.14%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	30.90%	68.90%	0.00%	0.17%	NA
Indica II	465	36.10%	63.70%	0.22%	0.00%	NA
Indica III	913	19.80%	79.70%	0.33%	0.11%	NA
Indica Intermediate	786	23.50%	75.80%	0.38%	0.25%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	62.20%	37.80%	0.00%	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
vg0329897160	A -> T	LOC_Os03g52090.1	intron_variant ; MODIFIER	silent_mutation	Average:50.514; most accessible tissue: Zhenshan97 young leaf, score: 72.747	N	N	N	N
vg0329897160	A -> DEL	N	N	silent_mutation	Average:50.514; most accessible tissue: Zhenshan97 young leaf, score: 72.747	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0329897160	NA	4.39E-14	mr1874	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
vg0329897160	NA	7.14E-14	mr1902	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
vg0329897160	NA	1.70E-06	mr1699_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
vg0329897160	4.71E-06	NA	mr1931_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