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Detailed information for vg0603482934:

Variant ID: vg0603482934 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 3482934
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTATCAATCTATATATTCCGGTGAATTACTTATTTATAAACACGATCATTATAGTGGTGATCATCATTTCATGTGTTCCTATATTTCATGTGGGATTGGA[T/C]
TCAAATGAATTGGATTTGATTTTACTGTTTCTTTTAGCTAATCATGGCATCAAGCTATCAACATGGTCCGAATATTTAATATTTGAACTATAAATTAAAT

Reverse complement sequence

ATTTAATTTATAGTTCAAATATTAAATATTCGGACCATGTTGATAGCTTGATGCCATGATTAGCTAAAAGAAACAGTAAAATCAAATCCAATTCATTTGA[A/G]
TCCAATCCCACATGAAATATAGGAACACATGAAATGATGATCACCACTATAATGATCGTGTTTATAAATAAGTAATTCACCGGAATATATAGATTGATAC

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	66.00%	0.40%	8.23%	25.35%	NA
All Indica	2759	75.50%	0.00%	3.81%	20.70%	NA
All Japonica	1512	40.70%	1.30%	18.06%	39.95%	NA
Aus	269	98.90%	0.00%	0.74%	0.37%	NA
Indica I	595	66.40%	0.00%	3.03%	30.59%	NA
Indica II	465	81.50%	0.00%	2.80%	15.70%	NA
Indica III	913	78.00%	0.00%	4.05%	17.96%	NA
Indica Intermediate	786	76.00%	0.00%	4.71%	19.34%	NA
Temperate Japonica	767	56.70%	0.30%	4.04%	38.98%	NA
Tropical Japonica	504	23.60%	3.00%	39.09%	34.33%	NA
Japonica Intermediate	241	25.70%	0.80%	18.67%	54.77%	NA
VI/Aromatic	96	91.70%	0.00%	7.29%	1.04%	NA
Intermediate	90	74.40%	0.00%	2.22%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0603482934	T -> C	LOC_Os06g07270.1	downstream_gene_variant ; 691.0bp to feature; MODIFIER	silent_mutation	Average:14.146; most accessible tissue: Callus, score: 41.206	N	N	N	N
vg0603482934	T -> C	LOC_Os06g07260-LOC_Os06g07270	intergenic_region ; MODIFIER	silent_mutation	Average:14.146; most accessible tissue: Callus, score: 41.206	N	N	N	N
vg0603482934	T -> DEL	N	N	silent_mutation	Average:14.146; most accessible tissue: Callus, score: 41.206	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0603482934	1.49E-06	NA	mr1392	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
vg0603482934	NA	9.21E-08	mr1408	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
vg0603482934	NA	2.88E-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