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Detailed information for vg1203462183:

Variant ID: vg1203462183 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3462183
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, A: 0.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

TATGATTAATAGTTCTAAAACTGCTTGATTTTCAGGCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGGTATTGAT[T/A]
TCATTTTTGCTGCGTGACACTAACCATGTAATCCAGTTATTTCAATGGCTTACCAATGACCGTGTTTGTGGTATTTCCTGATCAGGTTCGCCAAGGTACC

Reverse complement sequence

GGTACCTTGGCGAACCTGATCAGGAAATACCACAAACACGGTCATTGGTAAGCCATTGAAATAACTGGATTACATGGTTAGTGTCACGCAGCAAAAATGA[A/T]
ATCAATACCTTGACTGAAACGTTGCCCGTAAGGGTTGGTACTGTGACAGTTCCACCTAGTACAGCCTGAAAATCAAGCAGTTTTAGAACTATTAATCATA

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	87.90%	11.90%	0.15%	0.00%	NA
All Indica	2759	84.90%	14.90%	0.25%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	48.00%	52.00%	0.00%	0.00%	NA
Indica I	595	85.20%	14.60%	0.17%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	78.10%	21.50%	0.44%	0.00%	NA
Indica Intermediate	786	84.60%	15.10%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg1203462183	T -> A	LOC_Os12g07070.1	upstream_gene_variant ; 4269.0bp to feature; MODIFIER	silent_mutation	Average:70.701; most accessible tissue: Callus, score: 89.128	N	N	N	N
vg1203462183	T -> A	LOC_Os12g07060.1	intron_variant ; MODIFIER	silent_mutation	Average:70.701; most accessible tissue: Callus, score: 89.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203462183	4.50E-06	1.25E-06	mr1928	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
vg1203462183	NA	3.49E-06	mr1931	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