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Detailed information for vg0209814019:

Variant ID: vg0209814019 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9814019
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCATATATTCTTTCTCCCACTCTCTGAGAGGTTTAAATTTGTCGTCCATTGCGAGTTCACTCTGGTTGTCGTAGAAGAGACCTCTTGCATTGCAGACATC[G/A]
CGACGGATGAATCGGTAGAGGTCAGTGGCCACGTTCAAGATAAGTGGCCACGTTCAAGATAGTAGTGTCGTTGAATTGTTGTGCAATATATGGGATTTCG

Reverse complement sequence

CGAAATCCCATATATTGCACAACAATTCAACGACACTACTATCTTGAACGTGGCCACTTATCTTGAACGTGGCCACTGACCTCTACCGATTCATCCGTCG[C/T]
GATGTCTGCAATGCAAGAGGTCTCTTCTACGACAACCAGAGTGAACTCGCAATGGACGACAAATTTAAACCTCTCAGAGAGTGGGAGAAAGAATATATGC

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	72.20%	3.20%	3.64%	20.97%	NA
All Indica	2759	64.80%	0.10%	4.46%	30.59%	NA
All Japonica	1512	87.80%	9.60%	2.25%	0.40%	NA
Aus	269	51.30%	0.00%	3.35%	45.35%	NA
Indica I	595	64.40%	0.00%	3.03%	32.61%	NA
Indica II	465	55.70%	0.20%	8.17%	35.91%	NA
Indica III	913	69.90%	0.20%	4.38%	25.52%	NA
Indica Intermediate	786	64.80%	0.00%	3.44%	31.81%	NA
Temperate Japonica	767	91.90%	5.00%	2.74%	0.39%	NA
Tropical Japonica	504	80.80%	16.90%	1.79%	0.60%	NA
Japonica Intermediate	241	89.20%	9.10%	1.66%	0.00%	NA
VI/Aromatic	96	92.70%	0.00%	1.04%	6.25%	NA
Intermediate	90	77.80%	2.20%	5.56%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0209814019	G -> A	LOC_Os02g17130.1	upstream_gene_variant ; 3212.0bp to feature; MODIFIER	silent_mutation	Average:21.376; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N
vg0209814019	G -> A	LOC_Os02g17140.1	downstream_gene_variant ; 22.0bp to feature; MODIFIER	silent_mutation	Average:21.376; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N
vg0209814019	G -> A	LOC_Os02g17130-LOC_Os02g17140	intergenic_region ; MODIFIER	silent_mutation	Average:21.376; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N
vg0209814019	G -> DEL	N	N	silent_mutation	Average:21.376; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209814019	4.84E-06	4.84E-06	mr1264	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
vg0209814019	6.08E-06	NA	mr1949	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