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Detailed information for vg0818236084:

Variant ID: vg0818236084 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18236084
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGTGCATGGTTTTGCTGGTCGCACCCATGGCAGTTAAGGACCGGTTCGCGGGATGCCCTGGAAGAACTTATCGTACTTACCACAAGCCAGCGTGGGCAA[T/C]
GGCTGGGCTTGTAGCGTAGCTTTCCTCTAGCTGACGCATCCAGGCAAGGGTGGGCGTGATGGAGTTTGGATGGGCCCTGCGACGGCCTATGCGGCTTCCG

Reverse complement sequence

CGGAAGCCGCATAGGCCGTCGCAGGGCCCATCCAAACTCCATCACGCCCACCCTTGCCTGGATGCGTCAGCTAGAGGAAAGCTACGCTACAAGCCCAGCC[A/G]
TTGCCCACGCTGGCTTGTGGTAAGTACGATAAGTTCTTCCAGGGCATCCCGCGAACCGGTCCTTAACTGCCATGGGTGCGACCAGCAAAACCATGCACCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.70%	0.60%	6.16%	40.54%	NA
All Indica	2759	50.30%	0.90%	8.37%	40.41%	NA
All Japonica	1512	53.90%	0.00%	2.98%	43.12%	NA
Aus	269	51.70%	0.70%	4.09%	43.49%	NA
Indica I	595	47.60%	1.50%	9.24%	41.68%	NA
Indica II	465	88.00%	0.00%	1.51%	10.54%	NA
Indica III	913	33.30%	1.30%	11.06%	54.33%	NA
Indica Intermediate	786	49.70%	0.60%	8.65%	40.97%	NA
Temperate Japonica	767	82.30%	0.00%	0.39%	17.34%	NA
Tropical Japonica	504	14.70%	0.00%	6.55%	78.77%	NA
Japonica Intermediate	241	45.60%	0.00%	3.73%	50.62%	NA
VI/Aromatic	96	91.70%	0.00%	2.08%	6.25%	NA
Intermediate	90	67.80%	1.10%	2.22%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818236084	T -> C	LOC_Os08g29690.1	upstream_gene_variant ; 2193.0bp to feature; MODIFIER	silent_mutation	Average:31.105; most accessible tissue: Minghui63 flag leaf, score: 65.44	N	N	N	N
vg0818236084	T -> C	LOC_Os08g29700.1	downstream_gene_variant ; 3622.0bp to feature; MODIFIER	silent_mutation	Average:31.105; most accessible tissue: Minghui63 flag leaf, score: 65.44	N	N	N	N
vg0818236084	T -> C	LOC_Os08g29690-LOC_Os08g29700	intergenic_region ; MODIFIER	silent_mutation	Average:31.105; most accessible tissue: Minghui63 flag leaf, score: 65.44	N	N	N	N
vg0818236084	T -> DEL	N	N	silent_mutation	Average:31.105; most accessible tissue: Minghui63 flag leaf, score: 65.44	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818236084	1.96E-06	1.96E-06	mr1540	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