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Detailed information for vg0206920077:

Variant ID: vg0206920077 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6920077
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATATTGCGGTTGCAAAAAGTGTTTGTGATAGTTTCAGTCCATTGTATCAGGGTAGCCAGTTAATTTCTACCCAGTTGATGTACTATGTTCTTGTTTAGT[T/G]
TTTATCTTGTTGTGAAAGAAATCCTGTAGCATGAAATGGAGATTAGAAGACCCAATCTTATGCACATGGCTTTAATTAATCCAATCAAAGTGAATAAAAA

Reverse complement sequence

TTTTTATTCACTTTGATTGGATTAATTAAAGCCATGTGCATAAGATTGGGTCTTCTAATCTCCATTTCATGCTACAGGATTTCTTTCACAACAAGATAAA[A/C]
ACTAAACAAGAACATAGTACATCAACTGGGTAGAAATTAACTGGCTACCCTGATACAATGGACTGAAACTATCACAAACACTTTTTGCAACCGCAATATA

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	99.50%	0.30%	0.21%	0.00%	NA
All Indica	2759	99.80%	0.10%	0.11%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.07%	0.00%	NA
Aus	269	97.40%	1.50%	1.12%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0206920077	T -> G	LOC_Os02g13070.1	upstream_gene_variant ; 1628.0bp to feature; MODIFIER	N	Average:42.588; most accessible tissue: Minghui63 flower, score: 59.717	N	N	N	N
vg0206920077	T -> G	LOC_Os02g13080.1	upstream_gene_variant ; 909.0bp to feature; MODIFIER	N	Average:42.588; most accessible tissue: Minghui63 flower, score: 59.717	N	N	N	N
vg0206920077	T -> G	LOC_Os02g13060.1	downstream_gene_variant ; 3411.0bp to feature; MODIFIER	N	Average:42.588; most accessible tissue: Minghui63 flower, score: 59.717	N	N	N	N
vg0206920077	T -> G	LOC_Os02g13070-LOC_Os02g13080	intergenic_region ; MODIFIER	N	Average:42.588; most accessible tissue: Minghui63 flower, score: 59.717	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206920077	5.79E-06	1.74E-06	mr1682	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
vg0206920077	2.48E-06	NA	mr1754	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