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Detailed information for vg0207356509:

Variant ID: vg0207356509 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7356509
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGTTCCCAACCCATTCCAGCGAACACAGCCTAAGACGTTCAAAGGTTGGCCTTCTCAAACAACAAATATACTCCCTCCGTTTCGAAATGTTTGACGCC[A/G]
TTGACTTTTTATCACATGTTTGACCGTTCGTTTTATTCAAAAAATTTAAGTAATTATTAATTCTTTTCCTATCATTTAAGTATATAGCAGGCTAATTAAA

Reverse complement sequence

TTTAATTAGCCTGCTATATACTTAAATGATAGGAAAAGAATTAATAATTACTTAAATTTTTTGAATAAAACGAACGGTCAAACATGTGATAAAAAGTCAA[T/C]
GGCGTCAAACATTTCGAAACGGAGGGAGTATATTTGTTGTTTGAGAAGGCCAACCTTTGAACGTCTTAGGCTGTGTTCGCTGGAATGGGTTGGGAACCCA

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	59.00%	40.90%	0.15%	0.00%	NA
All Indica	2759	88.90%	11.00%	0.11%	0.00%	NA
All Japonica	1512	15.90%	83.90%	0.20%	0.00%	NA
Aus	269	14.50%	85.10%	0.37%	0.00%	NA
Indica I	595	96.00%	3.90%	0.17%	0.00%	NA
Indica II	465	83.20%	16.80%	0.00%	0.00%	NA
Indica III	913	88.10%	11.90%	0.00%	0.00%	NA
Indica Intermediate	786	87.90%	11.80%	0.25%	0.00%	NA
Temperate Japonica	767	11.30%	88.30%	0.39%	0.00%	NA
Tropical Japonica	504	19.60%	80.40%	0.00%	0.00%	NA
Japonica Intermediate	241	22.40%	77.60%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	57.80%	42.20%	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
vg0207356509	A -> G	LOC_Os02g13700-LOC_Os02g13710	intergenic_region ; MODIFIER	silent_mutation	Average:52.257; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207356509	NA	2.73E-09	mr1352	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
vg0207356509	NA	5.57E-07	mr1881	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
vg0207356509	NA	6.28E-06	mr1002_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
vg0207356509	NA	6.39E-09	mr1446_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