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Detailed information for vg0334584062:

Variant ID: vg0334584062 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34584062
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

AAAATAATTACATAAAGTGTGTACTAATGGCCATGATTAATTTGTCCGGTTCTTTCTTTTGTCTGAAGAACAATGAAATAATTTGTTCTAGTTCAAAAAA[A/G]
TCTATTGTATATATGACCTAATCTAAGCAGGTTTAATACATTTTTGATGGTTCTTGTCTTGAATCGTAAATGATGAATTGCTCTTCCTCATGCCAATATA

Reverse complement sequence

TATATTGGCATGAGGAAGAGCAATTCATCATTTACGATTCAAGACAAGAACCATCAAAAATGTATTAAACCTGCTTAGATTAGGTCATATATACAATAGA[T/C]
TTTTTTGAACTAGAACAAATTATTTCATTGTTCTTCAGACAAAAGAAAGAACCGGACAAATTAATCATGGCCATTAGTACACACTTTATGTAATTATTTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.00%	2.80%	1.23%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	87.70%	8.50%	3.84%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	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	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	77.10%	16.00%	6.91%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.40%	0.00%	NA
Japonica Intermediate	241	97.50%	1.20%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0334584062	A -> G	LOC_Os03g60850-LOC_Os03g60870	intergenic_region ; MODIFIER	silent_mutation	Average:43.459; most accessible tissue: Callus, score: 75.246	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334584062	NA	9.51E-07	mr1648	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
vg0334584062	NA	7.03E-06	mr1697	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
vg0334584062	8.92E-09	NA	mr1002_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