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Detailed information for vg0600544519:

Variant ID: vg0600544519 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 544519
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.02, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

CATAAATTGCAAAGTTGCTTCTCAGATAATTATGAGATTCAACCAAAATTTTGAATTCTGACCATCAATTATTTCTGATATGCTTAGTTTAAAAATAAAA[G/C]
AATTAACATATGTAGATTTGCCTCGAAAGTTACTACAATATCAGAAACTTATTATAATATAAAATTGATTGTTGGAATTTGATAAGTTTGACCGAATCTT

Reverse complement sequence

AAGATTCGGTCAAACTTATCAAATTCCAACAATCAATTTTATATTATAATAAGTTTCTGATATTGTAGTAACTTTCGAGGCAAATCTACATATGTTAATT[C/G]
TTTTATTTTTAAACTAAGCATATCAGAAATAATTGATGGTCAGAATTCAAAATTTTGGTTGAATCTCATAATTATCTGAGAAGCAACTTTGCAATTTATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.70%	24.00%	0.32%	0.00%	NA
All Indica	2759	63.20%	36.30%	0.51%	0.00%	NA
All Japonica	1512	97.70%	2.30%	0.00%	0.00%	NA
Aus	269	70.30%	29.70%	0.00%	0.00%	NA
Indica I	595	57.60%	42.00%	0.34%	0.00%	NA
Indica II	465	72.70%	26.70%	0.65%	0.00%	NA
Indica III	913	62.00%	37.80%	0.22%	0.00%	NA
Indica Intermediate	786	63.10%	36.00%	0.89%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	94.40%	5.60%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	17.80%	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
vg0600544519	G -> C	LOC_Os06g01972.1	upstream_gene_variant ; 1985.0bp to feature; MODIFIER	silent_mutation	Average:40.315; most accessible tissue: Callus, score: 64.59	N	N	N	N
vg0600544519	G -> C	LOC_Os06g01966.1	intron_variant ; MODIFIER	silent_mutation	Average:40.315; most accessible tissue: Callus, score: 64.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0600544519	4.67E-06	NA	mr1063	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
vg0600544519	4.61E-06	7.79E-07	mr1063	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
vg0600544519	NA	2.15E-06	mr1180	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
vg0600544519	NA	8.77E-06	mr1310	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
vg0600544519	NA	4.58E-06	mr1692	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
vg0600544519	NA	1.38E-06	mr1968	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