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Detailed information for vg0604026563:

Variant ID: vg0604026563 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 4026563
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATAATCATTTAGTTGACATATAATAAACGGGTGGACATCCACCCAAGTGATTAGAATCCATCTACGAAACAATATTCATTCCTTCAGGAAAGGTCCTCT[C/T]
GTTTTTTTCGCGTCGCTTAAAAAGTTAGCAAAGATTCTTTTAAAAAATCAGCTAGATAGATCAATATGTGACATGTCACTTCATAAAATGTATGTTCAAA

Reverse complement sequence

TTTGAACATACATTTTATGAAGTGACATGTCACATATTGATCTATCTAGCTGATTTTTTAAAAGAATCTTTGCTAACTTTTTAAGCGACGCGAAAAAAAC[G/A]
AGAGGACCTTTCCTGAAGGAATGAATATTGTTTCGTAGATGGATTCTAATCACTTGGGTGGATGTCCACCCGTTTATTATATGTCAACTAAATGATTATG

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	91.70%	8.20%	0.04%	0.00%	NA
All Indica	2759	93.00%	7.00%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	28.60%	71.40%	0.00%	0.00%	NA
Indica I	595	96.50%	3.40%	0.17%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	87.60%	12.40%	0.00%	0.00%	NA
Indica Intermediate	786	92.60%	7.30%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0604026563	C -> T	LOC_Os06g08300.2	downstream_gene_variant ; 3961.0bp to feature; MODIFIER	silent_mutation	Average:27.276; most accessible tissue: Callus, score: 57.097	N	N	N	N
vg0604026563	C -> T	LOC_Os06g08310.1	downstream_gene_variant ; 798.0bp to feature; MODIFIER	silent_mutation	Average:27.276; most accessible tissue: Callus, score: 57.097	N	N	N	N
vg0604026563	C -> T	LOC_Os06g08300-LOC_Os06g08310	intergenic_region ; MODIFIER	silent_mutation	Average:27.276; most accessible tissue: Callus, score: 57.097	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0604026563	1.19E-06	NA	mr1261	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
vg0604026563	NA	5.73E-06	mr1236_2	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