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Detailed information for vg0406946959:

Variant ID: vg0406946959 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6946959
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTAGTGGGCGCTCTACTCATGGTTCCCCTAGTATGAATTTAGATAGATGCTTCGCTGATTAATAAGACAACATTAGGTGGTTTTTATAACTTTAGACTT[T/C]
GGGAATATTCATATCTCTTGGACTTTATGGAATGGTTGGACTATTGTGGAATTGGATGCACACCTCTCCCTCTATTCAAAACTCTCAAAATGGTTATAGG

Reverse complement sequence

CCTATAACCATTTTGAGAGTTTTGAATAGAGGGAGAGGTGTGCATCCAATTCCACAATAGTCCAACCATTCCATAAAGTCCAAGAGATATGAATATTCCC[A/G]
AAGTCTAAAGTTATAAAAACCACCTAATGTTGTCTTATTAATCAGCGAAGCATCTATCTAAATTCATACTAGGGGAACCATGAGTAGAGCGCCCACTAGT

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	89.90%	0.30%	1.06%	8.74%	NA
All Indica	2759	84.40%	0.50%	1.78%	13.34%	NA
All Japonica	1512	99.80%	0.00%	0.00%	0.20%	NA
Aus	269	88.50%	0.00%	0.00%	11.52%	NA
Indica I	595	80.50%	0.20%	2.02%	17.31%	NA
Indica II	465	90.80%	0.20%	1.51%	7.53%	NA
Indica III	913	86.50%	0.80%	2.08%	10.62%	NA
Indica Intermediate	786	81.00%	0.60%	1.40%	16.92%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	94.80%	0.00%	0.00%	5.21%	NA
Intermediate	90	92.20%	0.00%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406946959	T -> C	LOC_Os04g12540.1	upstream_gene_variant ; 4243.0bp to feature; MODIFIER	silent_mutation	Average:11.319; most accessible tissue: Callus, score: 44.944	N	N	N	N
vg0406946959	T -> C	LOC_Os04g12550.1	downstream_gene_variant ; 4382.0bp to feature; MODIFIER	silent_mutation	Average:11.319; most accessible tissue: Callus, score: 44.944	N	N	N	N
vg0406946959	T -> C	LOC_Os04g12540-LOC_Os04g12550	intergenic_region ; MODIFIER	silent_mutation	Average:11.319; most accessible tissue: Callus, score: 44.944	N	N	N	N
vg0406946959	T -> DEL	N	N	silent_mutation	Average:11.319; most accessible tissue: Callus, score: 44.944	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406946959	4.31E-06	9.14E-06	mr1047_2	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