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Detailed information for vg1223326846:

Variant ID: vg1223326846 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23326846
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CAACGACGTTCACCGAACAATCGGACAGTGCATACCAGTTGCAGGTCCTCCTGCTCTGTCCATGGCCCTTTGCGTATCTCTTCTCTCACTGTCACCATAT[T/C]
GATTACCCTAGTATATGATGACAGTGTTGCACTAACGCTGCTCGCTCCTACCTTGTATCGGCTCGGAGCCGGTCTTCTTGCTCTTCTTCCACCTCTGTGT

Reverse complement sequence

ACACAGAGGTGGAAGAAGAGCAAGAAGACCGGCTCCGAGCCGATACAAGGTAGGAGCGAGCAGCGTTAGTGCAACACTGTCATCATATACTAGGGTAATC[A/G]
ATATGGTGACAGTGAGAGAAGAGATACGCAAAGGGCCATGGACAGAGCAGGAGGACCTGCAACTGGTATGCACTGTCCGATTGTTCGGTGAACGTCGTTG

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	55.00%	44.30%	0.08%	0.61%	NA
All Indica	2759	32.80%	66.20%	0.04%	0.94%	NA
All Japonica	1512	98.00%	1.70%	0.20%	0.07%	NA
Aus	269	24.90%	75.10%	0.00%	0.00%	NA
Indica I	595	18.00%	80.20%	0.00%	1.85%	NA
Indica II	465	40.40%	58.90%	0.00%	0.65%	NA
Indica III	913	36.70%	62.70%	0.00%	0.66%	NA
Indica Intermediate	786	35.10%	64.00%	0.13%	0.76%	NA
Temperate Japonica	767	97.10%	2.50%	0.39%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	66.70%	31.10%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223326846	T -> C	LOC_Os12g37970.1	5_prime_UTR_variant ; 3.0bp to feature; MODIFIER	silent_mutation	Average:79.678; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg1223326846	T -> C	LOC_Os12g37970.2	5_prime_UTR_variant ; 326.0bp to feature; MODIFIER	silent_mutation	Average:79.678; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg1223326846	T -> C	LOC_Os12g37970.3	5_prime_UTR_variant ; 326.0bp to feature; MODIFIER	silent_mutation	Average:79.678; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg1223326846	T -> C	LOC_Os12g37960.1	downstream_gene_variant ; 3093.0bp to feature; MODIFIER	silent_mutation	Average:79.678; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg1223326846	T -> C	LOC_Os12g37960.2	downstream_gene_variant ; 3093.0bp to feature; MODIFIER	silent_mutation	Average:79.678; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg1223326846	T -> DEL	N	N	silent_mutation	Average:79.678; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223326846	NA	6.42E-06	mr1425	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
vg1223326846	NA	5.42E-12	mr1902	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