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Detailed information for vg0612068302:

Variant ID: vg0612068302 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12068302
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

ATCATTGTCGGAGCCTGACACTGCGTAACTTGGGATGGTCGGCAAGCATGTCCAGATTTTTCTGTCTCAACTTGGTGCCACTCAAAGCTACCTTGGTAAG[C/T]
TCATTGCTACCTTTTGCCAATAATGAGAGAATCCGTAGATTTGTGGATCCGTTGATGCTTACACTCTCCAGAAGCTTCGGTGGATGTATCAAGCGGTTGT

Reverse complement sequence

ACAACCGCTTGATACATCCACCGAAGCTTCTGGAGAGTGTAAGCATCAACGGATCCACAAATCTACGGATTCTCTCATTATTGGCAAAAGGTAGCAATGA[G/A]
CTTACCAAGGTAGCTTTGAGTGGCACCAAGTTGAGACAGAAAAATCTGGACATGCTTGCCGACCATCCCAAGTTACGCAGTGTCAGGCTCCGACAATGAT

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	96.00%	3.60%	0.04%	0.28%	NA
All Indica	2759	96.80%	3.10%	0.00%	0.11%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	95.20%	1.10%	0.00%	3.72%	NA
Indica I	595	95.80%	4.20%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	96.70%	3.20%	0.00%	0.11%	NA
Indica Intermediate	786	96.10%	3.70%	0.00%	0.25%	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	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	30.20%	69.80%	0.00%	0.00%	NA
Intermediate	90	86.70%	11.10%	2.22%	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
vg0612068302	C -> T	LOC_Os06g20879.1	downstream_gene_variant ; 3003.0bp to feature; MODIFIER	silent_mutation	Average:63.751; most accessible tissue: Callus, score: 87.26	N	N	N	N
vg0612068302	C -> T	LOC_Os06g20879.2	downstream_gene_variant ; 2955.0bp to feature; MODIFIER	silent_mutation	Average:63.751; most accessible tissue: Callus, score: 87.26	N	N	N	N
vg0612068302	C -> T	LOC_Os06g20879-LOC_Os06g20890	intergenic_region ; MODIFIER	silent_mutation	Average:63.751; most accessible tissue: Callus, score: 87.26	N	N	N	N
vg0612068302	C -> DEL	N	N	silent_mutation	Average:63.751; most accessible tissue: Callus, score: 87.26	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612068302	3.62E-06	7.54E-06	mr1401	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
vg0612068302	NA	1.05E-09	mr1570	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