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Detailed information for vg0703290612:

Variant ID: vg0703290612 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3290612
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

ACATAAAAGGTCCATTCTCACGTACTGTTAAACTTATCAGAACCACAAAATTTGGATGAGATACAATAGATTTACAAATAACCACTACCAACGTCAGAAA[A/G]
TCTTTGCAAGCTGCTAAAAAAGGATGTCAAATACACATATTTTAACAACTATCGTCAAGTTTGGTATTTGAATACACTAGCTTAACAGAGTGTTTCAAGA

Reverse complement sequence

TCTTGAAACACTCTGTTAAGCTAGTGTATTCAAATACCAAACTTGACGATAGTTGTTAAAATATGTGTATTTGACATCCTTTTTTAGCAGCTTGCAAAGA[T/C]
TTTCTGACGTTGGTAGTGGTTATTTGTAAATCTATTGTATCTCATCCAAATTTTGTGGTTCTGATAAGTTTAACAGTACGTGAGAATGGACCTTTTATGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.00%	49.70%	0.32%	0.00%	NA
All Indica	2759	76.50%	23.10%	0.40%	0.00%	NA
All Japonica	1512	0.30%	99.70%	0.00%	0.00%	NA
Aus	269	75.50%	24.50%	0.00%	0.00%	NA
Indica I	595	59.00%	40.70%	0.34%	0.00%	NA
Indica II	465	92.00%	7.50%	0.43%	0.00%	NA
Indica III	913	79.60%	20.30%	0.11%	0.00%	NA
Indica Intermediate	786	77.10%	22.10%	0.76%	0.00%	NA
Temperate Japonica	767	0.10%	99.90%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	0.00%	100.00%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	92.70%	1.04%	0.00%	NA
Intermediate	90	38.90%	57.80%	3.33%	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
vg0703290612	A -> G	LOC_Os07g06730.1	downstream_gene_variant ; 3185.0bp to feature; MODIFIER	silent_mutation	Average:38.789; most accessible tissue: Zhenshan97 young leaf, score: 59.009	N	N	N	N
vg0703290612	A -> G	LOC_Os07g06740.1	intron_variant ; MODIFIER	silent_mutation	Average:38.789; most accessible tissue: Zhenshan97 young leaf, score: 59.009	N	N	N	N
vg0703290612	A -> G	LOC_Os07g06740.3	intron_variant ; MODIFIER	silent_mutation	Average:38.789; most accessible tissue: Zhenshan97 young leaf, score: 59.009	N	N	N	N
vg0703290612	A -> G	LOC_Os07g06740.2	intron_variant ; MODIFIER	silent_mutation	Average:38.789; most accessible tissue: Zhenshan97 young leaf, score: 59.009	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703290612	4.52E-06	4.52E-06	mr1192_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
vg0703290612	NA	1.69E-08	mr1274_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
vg0703290612	NA	8.79E-06	mr1364_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
vg0703290612	NA	2.95E-06	mr1780_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