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Detailed information for vg1224662551:

Variant ID: vg1224662551 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24662551
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, C: 0.06, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTAGAGTTTTGAGTTTAGTCGAGATTTTTGTGAGGAGTGTTGTTGTTGCACTTTGTAAACACAGAGAGAAGTAATAAAGTTGTCATCTACATCAAGAG[C/T]
TATTCGATTTATGTTTGCTCAGGTTCGGCGGTCTAACCGGTGAGACACCGGCGGTCAGACCGGTGGCATCACGGCGATCAGACAGGCGGGTACATGGCGG

Reverse complement sequence

CCGCCATGTACCCGCCTGTCTGATCGCCGTGATGCCACCGGTCTGACCGCCGGTGTCTCACCGGTTAGACCGCCGAACCTGAGCAAACATAAATCGAATA[G/A]
CTCTTGATGTAGATGACAACTTTATTACTTCTCTCTGTGTTTACAAAGTGCAACAACAACACTCCTCACAAAAATCTCGACTAAACTCAAAACTCTAACT

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	69.60%	30.10%	0.30%	0.00%	NA
All Indica	2759	98.40%	1.40%	0.18%	0.00%	NA
All Japonica	1512	14.10%	85.40%	0.53%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	96.60%	3.00%	0.43%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	97.30%	2.40%	0.25%	0.00%	NA
Temperate Japonica	767	5.10%	94.50%	0.39%	0.00%	NA
Tropical Japonica	504	28.60%	70.60%	0.79%	0.00%	NA
Japonica Intermediate	241	12.40%	87.10%	0.41%	0.00%	NA
VI/Aromatic	96	42.70%	57.30%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	1.11%	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
vg1224662551	C -> T	LOC_Os12g39910.1	downstream_gene_variant ; 4301.0bp to feature; MODIFIER	silent_mutation	Average:48.257; most accessible tissue: Minghui63 flag leaf, score: 58.568	N	N	N	N
vg1224662551	C -> T	LOC_Os12g39910-LOC_Os12g39920	intergenic_region ; MODIFIER	silent_mutation	Average:48.257; most accessible tissue: Minghui63 flag leaf, score: 58.568	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224662551	NA	8.72E-45	mr1563	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
vg1224662551	5.54E-06	NA	mr1489_2	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
vg1224662551	NA	2.09E-17	mr1790_2	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