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Detailed information for vg0334285053:

Variant ID: vg0334285053 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34285053
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.58, A: 0.42, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAATGCTCCATGCATGTGTCCAAACATTTGATGTGACGGAAAAGTTGAAAGTTTGAAGGGAACTAAACACAGCTTAAGGCCTTGTTTAGATAAAAAAA[A/T]
TTGGCCAAAAACATCACATCAAATGTTTGACACATGCATGGGGCATTAAATGTGGGGAAAAAAATCAATTGCACAGTTTACATGTAAATTGCGAGACGAA

Reverse complement sequence

TTCGTCTCGCAATTTACATGTAAACTGTGCAATTGATTTTTTTCCCCACATTTAATGCCCCATGCATGTGTCAAACATTTGATGTGATGTTTTTGGCCAA[T/A]
TTTTTTTATCTAAACAAGGCCTTAAGCTGTGTTTAGTTCCCTTCAAACTTTCAACTTTTCCGTCACATCAAATGTTTGGACACATGCATGGAGCATTAAA

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	57.30%	42.50%	0.21%	0.00%	NA
All Indica	2759	85.70%	14.00%	0.33%	0.00%	NA
All Japonica	1512	2.00%	98.00%	0.00%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	97.50%	2.20%	0.34%	0.00%	NA
Indica II	465	86.70%	13.10%	0.22%	0.00%	NA
Indica III	913	83.80%	16.20%	0.00%	0.00%	NA
Indica Intermediate	786	78.50%	20.70%	0.76%	0.00%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	4.80%	95.20%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	46.70%	52.20%	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
vg0334285053	A -> T	LOC_Os03g60300.1	downstream_gene_variant ; 4805.0bp to feature; MODIFIER	silent_mutation	Average:37.422; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0334285053	A -> T	LOC_Os03g60279.1	intron_variant ; MODIFIER	silent_mutation	Average:37.422; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334285053	NA	4.70E-07	mr1646	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
vg0334285053	NA	7.18E-13	mr1924	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
vg0334285053	3.28E-06	NA	mr1671_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
vg0334285053	3.91E-07	7.17E-06	mr1671_2	Ind_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