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Detailed information for vg1223866012:

Variant ID: vg1223866012 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23866012
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.57, T: 0.44, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCTGGATCGTCTCGTCTAATCTTGTATCGTAGTGCTTTGCAAACAGGGCATGCTTCTAGGTTCTCGTACTCCTCACCGCAATATAGGATACAATCATT[T/C]
GGACATGCGTGAATCTTCTGAACTTACAGTCCTAGAGGGCAGACTATCTTCTCAGCCTCGTACGTTGTCTCGGGCAATTTGTTTCTCTTCGGAAGAATGT

Reverse complement sequence

ACATTCTTCCGAAGAGAAACAAATTGCCCGAGACAACGTACGAGGCTGAGAAGATAGTCTGCCCTCTAGGACTGTAAGTTCAGAAGATTCACGCATGTCC[A/G]
AATGATTGTATCCTATATTGCGGTGAGGAGTACGAGAACCTAGAAGCATGCCCTGTTTGCAAAGCACTACGATACAAGATTAGACGAGACGATCCAGGAG

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	44.90%	31.90%	18.96%	4.27%	NA
All Indica	2759	71.10%	7.10%	20.62%	1.20%	NA
All Japonica	1512	0.50%	77.60%	10.98%	10.98%	NA
Aus	269	43.90%	3.30%	52.79%	0.00%	NA
Indica I	595	87.20%	3.50%	9.24%	0.00%	NA
Indica II	465	60.20%	14.60%	24.95%	0.22%	NA
Indica III	913	78.10%	4.30%	15.55%	2.08%	NA
Indica Intermediate	786	57.30%	8.50%	32.57%	1.65%	NA
Temperate Japonica	767	0.30%	85.30%	4.95%	9.52%	NA
Tropical Japonica	504	1.00%	73.80%	17.46%	7.74%	NA
Japonica Intermediate	241	0.00%	61.00%	16.60%	22.41%	NA
VI/Aromatic	96	6.20%	88.50%	5.21%	0.00%	NA
Intermediate	90	30.00%	51.10%	15.56%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223866012	T -> C	LOC_Os12g38840.1	intron_variant ; MODIFIER	silent_mutation	Average:10.116; most accessible tissue: Callus, score: 26.731	N	N	N	N
vg1223866012	T -> DEL	N	N	silent_mutation	Average:10.116; most accessible tissue: Callus, score: 26.731	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223866012	NA	4.89E-07	mr1278	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
vg1223866012	NA	2.04E-09	mr1645_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
vg1223866012	NA	4.15E-07	mr1648_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
vg1223866012	2.05E-06	1.65E-20	mr1657_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
vg1223866012	1.42E-06	NA	mr1851_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