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Detailed information for vg0312485967:

Variant ID: vg0312485967 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 12485967
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTATATATGATGTTTCAATTTTTTTTTGCTGGTAGTTGGCTATATTATTAAACTTACTCTTAGGTACAACCACTACTAACATAAAAATAAAGAAAAAAA[A/T]
ATAATCACCTTCTCAGTTAGATCACCTCGATGTATGCAAGTAATATAATTGGGGTTTAATAGTAGATGATGCAGAAGAGATGCGAGTTAATGTATGCATG

Reverse complement sequence

CATGCATACATTAACTCGCATCTCTTCTGCATCATCTACTATTAAACCCCAATTATATTACTTGCATACATCGAGGTGATCTAACTGAGAAGGTGATTAT[T/A]
TTTTTTTCTTTATTTTTATGTTAGTAGTGGTTGTACCTAAGAGTAAGTTTAATAATATAGCCAACTACCAGCAAAAAAAAATTGAAACATCATATATAGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.40%	39.50%	0.08%	0.04%	NA
All Indica	2759	92.40%	7.50%	0.04%	0.07%	NA
All Japonica	1512	1.70%	98.30%	0.00%	0.00%	NA
Aus	269	85.10%	14.90%	0.00%	0.00%	NA
Indica I	595	84.00%	15.80%	0.00%	0.17%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	95.80%	4.20%	0.00%	0.00%	NA
Indica Intermediate	786	91.20%	8.50%	0.13%	0.13%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	3.00%	97.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	44.40%	52.20%	3.33%	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
vg0312485967	A -> T	LOC_Os03g21840.1	upstream_gene_variant ; 2869.0bp to feature; MODIFIER	silent_mutation	Average:36.885; most accessible tissue: Callus, score: 64.662	N	N	N	N
vg0312485967	A -> T	LOC_Os03g21840-LOC_Os03g21850	intergenic_region ; MODIFIER	silent_mutation	Average:36.885; most accessible tissue: Callus, score: 64.662	N	N	N	N
vg0312485967	A -> DEL	N	N	silent_mutation	Average:36.885; most accessible tissue: Callus, score: 64.662	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0312485967	NA	1.24E-36	mr1064	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
vg0312485967	NA	1.33E-41	mr1534	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
vg0312485967	2.56E-06	NA	mr1973_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