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Detailed information for vg0304795782:

Variant ID: vg0304795782 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 4795782
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTCTCTTTCTTTTTTTCCCATCCATATGCTTCCCTTCCTTTATTACTATATCATGCGTCTTCATGAGACGATTTAATCAAAAGAATTTTTAGTATCTT[G/A]
CACTCGCATTTTTAATTTGTGACCATACTACACGGTATGTATATACATGTACTGTATGATAATTAACTAGCAATAGTTTCTTATTTACTCGAGAAAAAAA

Reverse complement sequence

TTTTTTTCTCGAGTAAATAAGAAACTATTGCTAGTTAATTATCATACAGTACATGTATATACATACCGTGTAGTATGGTCACAAATTAAAAATGCGAGTG[C/T]
AAGATACTAAAAATTCTTTTGATTAAATCGTCTCATGAAGACGCATGATATAGTAATAAAGGAAGGGAAGCATATGGATGGGAAAAAAAGAAAGAGAAAA

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	35.90%	3.40%	14.77%	45.96%	NA
All Indica	2759	3.20%	5.20%	20.70%	70.93%	NA
All Japonica	1512	99.50%	0.00%	0.20%	0.26%	NA
Aus	269	3.00%	4.10%	38.66%	54.28%	NA
Indica I	595	2.40%	3.40%	13.95%	80.34%	NA
Indica II	465	9.50%	4.70%	22.80%	63.01%	NA
Indica III	913	0.50%	8.30%	21.91%	69.22%	NA
Indica Intermediate	786	3.20%	3.20%	23.16%	70.48%	NA
Temperate Japonica	767	99.50%	0.00%	0.13%	0.39%	NA
Tropical Japonica	504	99.60%	0.00%	0.40%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	52.10%	3.10%	9.38%	35.42%	NA
Intermediate	90	51.10%	2.20%	12.22%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0304795782	G -> A	LOC_Os03g09190.1	downstream_gene_variant ; 2636.0bp to feature; MODIFIER	silent_mutation	Average:10.662; most accessible tissue: Callus, score: 42.907	N	N	N	N
vg0304795782	G -> A	LOC_Os03g09190.2	downstream_gene_variant ; 2636.0bp to feature; MODIFIER	silent_mutation	Average:10.662; most accessible tissue: Callus, score: 42.907	N	N	N	N
vg0304795782	G -> A	LOC_Os03g09200.1	intron_variant ; MODIFIER	silent_mutation	Average:10.662; most accessible tissue: Callus, score: 42.907	N	N	N	N
vg0304795782	G -> DEL	N	N	silent_mutation	Average:10.662; most accessible tissue: Callus, score: 42.907	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0304795782	NA	3.49E-10	mr1005	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
vg0304795782	8.64E-06	NA	mr1265	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
vg0304795782	NA	1.39E-09	mr1277	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
vg0304795782	NA	5.14E-86	mr1758	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