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Detailed information for vg1206658127:

Variant ID: vg1206658127 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6658127
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.01, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

GCAATAGGTGCCGACCAATTGGAGCCGGACGGGAAACCGGTACCTATTGCCAGTTCCCAACCGGCGCCAATAGGTTTTTTTTACTAGCGACATAATCAGA[C/T]
CAATGGAAGTTATTTCCGTGGTTATTTTCGGTTGTTGCCAATACAATACAGAATCCTCTTTGATCATTATTACGTGATATTTATGATAAAATCTAATAAA

Reverse complement sequence

TTTATTAGATTTTATCATAAATATCACGTAATAATGATCAAAGAGGATTCTGTATTGTATTGGCAACAACCGAAAATAACCACGGAAATAACTTCCATTG[G/A]
TCTGATTATGTCGCTAGTAAAAAAAACCTATTGGCGCCGGTTGGGAACTGGCAATAGGTACCGGTTTCCCGTCCGGCTCCAATTGGTCGGCACCTATTGC

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	31.20%	8.70%	0.08%	59.97%	NA
All Indica	2759	6.00%	2.30%	0.11%	91.59%	NA
All Japonica	1512	73.70%	22.60%	0.07%	3.70%	NA
Aus	269	49.10%	1.10%	0.00%	49.81%	NA
Indica I	595	4.90%	3.70%	0.17%	91.26%	NA
Indica II	465	4.70%	4.10%	0.00%	91.18%	NA
Indica III	913	3.80%	0.80%	0.22%	95.18%	NA
Indica Intermediate	786	10.20%	1.90%	0.00%	87.91%	NA
Temperate Japonica	767	69.40%	25.80%	0.13%	4.69%	NA
Tropical Japonica	504	92.30%	5.00%	0.00%	2.78%	NA
Japonica Intermediate	241	48.50%	49.00%	0.00%	2.49%	NA
VI/Aromatic	96	13.50%	0.00%	0.00%	86.46%	NA
Intermediate	90	56.70%	5.60%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206658127	C -> DEL	N	N	silent_mutation	Average:17.941; most accessible tissue: Callus, score: 52.377	N	N	N	N
vg1206658127	C -> T	LOC_Os12g12140.1	upstream_gene_variant ; 197.0bp to feature; MODIFIER	silent_mutation	Average:17.941; most accessible tissue: Callus, score: 52.377	N	N	N	N
vg1206658127	C -> T	LOC_Os12g12150.1	upstream_gene_variant ; 3181.0bp to feature; MODIFIER	silent_mutation	Average:17.941; most accessible tissue: Callus, score: 52.377	N	N	N	N
vg1206658127	C -> T	LOC_Os12g12130.1	downstream_gene_variant ; 3888.0bp to feature; MODIFIER	silent_mutation	Average:17.941; most accessible tissue: Callus, score: 52.377	N	N	N	N
vg1206658127	C -> T	LOC_Os12g12140-LOC_Os12g12150	intergenic_region ; MODIFIER	silent_mutation	Average:17.941; most accessible tissue: Callus, score: 52.377	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206658127	3.17E-06	NA	mr1067	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