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Detailed information for vg0203405727:

Variant ID: vg0203405727 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3405727
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCCGGGAAGAATTTCTCGGTCGGTCACCCATCCCAAATTGCTCCAGGCCAAACACGCTTAACCCTGGAGTTCTTTGGAGATCGGTTTCCAGAAAAGAA[G/A]
TTGCAACTTGTTGATATGAGTATTCTATTAATCCTATTAAGTCCTGGGATGTCACAAGCAGATAGAAACCTCTCACACCAATCTGTTAATCTCTTAGAAA

Reverse complement sequence

TTTCTAAGAGATTAACAGATTGGTGTGAGAGGTTTCTATCTGCTTGTGACATCCCAGGACTTAATAGGATTAATAGAATACTCATATCAACAAGTTGCAA[C/T]
TTCTTTTCTGGAAACCGATCTCCAAAGAACTCCAGGGTTAAGCGTGTTTGGCCTGGAGCAATTTGGGATGGGTGACCGACCGAGAAATTCTTCCCGGGTG

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	25.00%	6.70%	1.10%	67.25%	NA
All Indica	2759	6.80%	3.30%	1.45%	88.44%	NA
All Japonica	1512	61.80%	0.10%	0.66%	37.37%	NA
Aus	269	5.60%	79.90%	0.00%	14.50%	NA
Indica I	595	11.90%	0.20%	1.85%	86.05%	NA
Indica II	465	5.40%	0.40%	1.94%	92.26%	NA
Indica III	913	3.90%	6.10%	0.88%	89.05%	NA
Indica Intermediate	786	7.10%	4.10%	1.53%	87.28%	NA
Temperate Japonica	767	71.30%	0.00%	0.78%	27.90%	NA
Tropical Japonica	504	54.80%	0.20%	0.40%	44.64%	NA
Japonica Intermediate	241	46.50%	0.40%	0.83%	52.28%	NA
VI/Aromatic	96	5.20%	2.10%	1.04%	91.67%	NA
Intermediate	90	41.10%	6.70%	1.11%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203405727	G -> A	LOC_Os02g06754.1	upstream_gene_variant ; 2297.0bp to feature; MODIFIER	silent_mutation	Average:10.995; most accessible tissue: Callus, score: 21.263	N	N	N	N
vg0203405727	G -> A	LOC_Os02g06750.1	intron_variant ; MODIFIER	silent_mutation	Average:10.995; most accessible tissue: Callus, score: 21.263	N	N	N	N
vg0203405727	G -> DEL	N	N	silent_mutation	Average:10.995; most accessible tissue: Callus, score: 21.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203405727	NA	3.62E-08	mr1465	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
vg0203405727	3.63E-06	NA	mr1793_2	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