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Detailed information for vg1213006164:

Variant ID: vg1213006164 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13006164
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

AGAAAGTCCAGCGACCAATCTACTTCATTAGCGAGGTTTTGGCCGACTCCAAGATGAGATATCCCCAAGTTCAGAAGCTGTTATATGGTGTTCTAATTAC[C/T]
GTCAGGAAATTATCTCACTACTTCCAAGGTCACTCGGTCACGGTGGTTACATCGTTTCCACTCGGCAATATACTCCATAATCGTGAAGCAAACGGGTGGA

Reverse complement sequence

TCCACCCGTTTGCTTCACGATTATGGAGTATATTGCCGAGTGGAAACGATGTAACCACCGTGACCGAGTGACCTTGGAAGTAGTGAGATAATTTCCTGAC[G/A]
GTAATTAGAACACCATATAACAGCTTCTGAACTTGGGGATATCTCATCTTGGAGTCGGCCAAAACCTCGCTAATGAAGTAGATTGGTCGCTGGACTTTCT

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	78.40%	21.60%	0.02%	0.00%	NA
All Indica	2759	64.40%	35.50%	0.04%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	61.80%	38.20%	0.00%	0.00%	NA
Indica II	465	77.80%	22.20%	0.00%	0.00%	NA
Indica III	913	55.00%	44.90%	0.11%	0.00%	NA
Indica Intermediate	786	69.50%	30.50%	0.00%	0.00%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg1213006164	C -> T	LOC_Os12g22990.1	upstream_gene_variant ; 3235.0bp to feature; MODIFIER	silent_mutation	Average:54.699; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg1213006164	C -> T	LOC_Os12g23010.1	downstream_gene_variant ; 2349.0bp to feature; MODIFIER	silent_mutation	Average:54.699; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg1213006164	C -> T	LOC_Os12g22990-LOC_Os12g23010	intergenic_region ; MODIFIER	silent_mutation	Average:54.699; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213006164	NA	9.22E-07	mr1671	Ind_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
vg1213006164	4.78E-06	4.78E-06	mr1688	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