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Detailed information for vg0209100423:

Variant ID: vg0209100423 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9100423
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTAAATGTATCGAACCCTTTTCTCCTATTTCCTCAAAAAATTGACCATTGAGTAGGGAAACACTGCATTTAAAGCAGTTTTTTTAGGGAGGGGGGGGGG[T/G]
GGGCTGGCTAAAAGGGTGGTTAAAAGAATTCGTTGTTGGTTGGACACCGGATAAATTTAGTCTTTTTGACAACAAACCGAGTGAAATGGAGGAGGAAGCA

Reverse complement sequence

TGCTTCCTCCTCCATTTCACTCGGTTTGTTGTCAAAAAGACTAAATTTATCCGGTGTCCAACCAACAACGAATTCTTTTAACCACCCTTTTAGCCAGCCC[A/C]
CCCCCCCCCCTCCCTAAAAAAACTGCTTTAAATGCAGTGTTTCCCTACTCAATGGTCAATTTTTTGAGGAAATAGGAGAAAAGGGTTCGATACATTTACA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.60%	1.20%	5.71%	2.50%	NA
All Indica	2759	87.80%	0.80%	7.36%	4.06%	NA
All Japonica	1512	97.20%	1.90%	0.73%	0.20%	NA
Aus	269	79.60%	1.50%	18.22%	0.74%	NA
Indica I	595	78.20%	0.50%	20.17%	1.18%	NA
Indica II	465	93.50%	0.40%	2.37%	3.66%	NA
Indica III	913	88.10%	1.30%	2.74%	7.89%	NA
Indica Intermediate	786	91.50%	0.50%	5.98%	2.04%	NA
Temperate Japonica	767	98.30%	1.20%	0.52%	0.00%	NA
Tropical Japonica	504	95.60%	3.00%	0.79%	0.60%	NA
Japonica Intermediate	241	97.10%	1.70%	1.24%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	92.20%	0.00%	6.67%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0209100423	T -> G	LOC_Os02g16020.1	upstream_gene_variant ; 1594.0bp to feature; MODIFIER	silent_mutation	Average:51.796; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0209100423	T -> G	LOC_Os02g16010.1	downstream_gene_variant ; 4708.0bp to feature; MODIFIER	silent_mutation	Average:51.796; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0209100423	T -> G	LOC_Os02g16020-LOC_Os02g16030	intergenic_region ; MODIFIER	silent_mutation	Average:51.796; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0209100423	T -> DEL	N	N	silent_mutation	Average:51.796; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209100423	1.58E-06	1.58E-06	mr1828_2	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