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Detailed information for vg1208828240:

Variant ID: vg1208828240 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8828240
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGAGACACGGTGGCAACCAACTGCGTGAATATTTTTTTTTTCAATTTTTGATCCAACTCCTTGTGCAAGAGGTGCGAAAAAAATGGCAACCAACTGCG[C/T]
GAAAATGAAGTCTCGAAAAAAGATAATAAAAAAAGGGAAAATGGGCCACGCACGACTGTGTGAGGGATAGGCTCAAAACGCACGCCACTTAAATTCGCGG

Reverse complement sequence

CCGCGAATTTAAGTGGCGTGCGTTTTGAGCCTATCCCTCACACAGTCGTGCGTGGCCCATTTTCCCTTTTTTTATTATCTTTTTTCGAGACTTCATTTTC[G/A]
CGCAGTTGGTTGCCATTTTTTTCGCACCTCTTGCACAAGGAGTTGGATCAAAAATTGAAAAAAAAAATATTCACGCAGTTGGTTGCCACCGTGTCTCCTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.80%	3.50%	20.02%	17.73%	NA
All Indica	2759	46.10%	0.40%	28.63%	24.79%	NA
All Japonica	1512	81.50%	8.90%	7.21%	2.45%	NA
Aus	269	69.10%	1.10%	2.97%	26.77%	NA
Indica I	595	37.00%	0.00%	24.37%	38.66%	NA
Indica II	465	41.10%	0.00%	35.27%	23.66%	NA
Indica III	913	58.70%	0.70%	24.32%	16.32%	NA
Indica Intermediate	786	41.50%	0.80%	32.95%	24.81%	NA
Temperate Japonica	767	79.40%	6.40%	10.17%	4.04%	NA
Tropical Japonica	504	90.30%	6.50%	2.58%	0.60%	NA
Japonica Intermediate	241	69.70%	21.60%	7.47%	1.24%	NA
VI/Aromatic	96	29.20%	14.60%	28.12%	28.12%	NA
Intermediate	90	64.40%	2.20%	13.33%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208828240	C -> DEL	N	N	silent_mutation	Average:33.591; most accessible tissue: Callus, score: 68.448	N	N	N	N
vg1208828240	C -> T	LOC_Os12g15460.1	upstream_gene_variant ; 1112.0bp to feature; MODIFIER	silent_mutation	Average:33.591; most accessible tissue: Callus, score: 68.448	N	N	N	N
vg1208828240	C -> T	LOC_Os12g15470.1	downstream_gene_variant ; 1283.0bp to feature; MODIFIER	silent_mutation	Average:33.591; most accessible tissue: Callus, score: 68.448	N	N	N	N
vg1208828240	C -> T	LOC_Os12g15470.2	downstream_gene_variant ; 1283.0bp to feature; MODIFIER	silent_mutation	Average:33.591; most accessible tissue: Callus, score: 68.448	N	N	N	N
vg1208828240	C -> T	LOC_Os12g15470.3	downstream_gene_variant ; 2507.0bp to feature; MODIFIER	silent_mutation	Average:33.591; most accessible tissue: Callus, score: 68.448	N	N	N	N
vg1208828240	C -> T	LOC_Os12g15460-LOC_Os12g15470	intergenic_region ; MODIFIER	silent_mutation	Average:33.591; most accessible tissue: Callus, score: 68.448	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208828240	1.46E-06	3.40E-09	mr1619	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
vg1208828240	NA	9.25E-06	mr1913	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