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Detailed information for vg0412124666:

Variant ID: vg0412124666 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12124666
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

CACTGGAGGATCGTTCATGCACAAAACACCGTCAGAAGGAAGAATAATGTTGGATCGCATTCTAGAAAATACTTCCTTCATGACGCAAACCAATGAAAAC[C/T]
AGTCGAAGGCATCAGTGTCCAAGATAGAGGAACCTCTAACGATGAAGCCACTCGCTCAACCATCCACTTCTGCTAGCTCGATTGATGAAAAGGTTCCTGA

Reverse complement sequence

TCAGGAACCTTTTCATCAATCGAGCTAGCAGAAGTGGATGGTTGAGCGAGTGGCTTCATCGTTAGAGGTTCCTCTATCTTGGACACTGATGCCTTCGACT[G/A]
GTTTTCATTGGTTTGCGTCATGAAGGAAGTATTTTCTAGAATGCGATCCAACATTATTCTTCCTTCTGACGGTGTTTTGTGCATGAACGATCCTCCAGTG

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	59.10%	22.10%	0.23%	18.54%	NA
All Indica	2759	93.40%	5.70%	0.14%	0.69%	NA
All Japonica	1512	2.10%	47.50%	0.13%	50.26%	NA
Aus	269	48.30%	50.60%	0.00%	1.12%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	96.60%	1.70%	0.43%	1.29%	NA
Indica III	913	87.80%	11.50%	0.11%	0.55%	NA
Indica Intermediate	786	93.40%	5.60%	0.13%	0.89%	NA
Temperate Japonica	767	0.70%	80.40%	0.00%	18.90%	NA
Tropical Japonica	504	3.00%	3.80%	0.20%	93.06%	NA
Japonica Intermediate	241	5.00%	34.00%	0.41%	60.58%	NA
VI/Aromatic	96	7.30%	13.50%	3.12%	76.04%	NA
Intermediate	90	53.30%	21.10%	2.22%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412124666	C -> DEL	N	N	silent_mutation	Average:63.84; most accessible tissue: Minghui63 young leaf, score: 76.385	N	N	N	N
vg0412124666	C -> T	LOC_Os04g21430.1	upstream_gene_variant ; 4952.0bp to feature; MODIFIER	silent_mutation	Average:63.84; most accessible tissue: Minghui63 young leaf, score: 76.385	N	N	N	N
vg0412124666	C -> T	LOC_Os04g21450.1	downstream_gene_variant ; 2010.0bp to feature; MODIFIER	silent_mutation	Average:63.84; most accessible tissue: Minghui63 young leaf, score: 76.385	N	N	N	N
vg0412124666	C -> T	LOC_Os04g21430-LOC_Os04g21450	intergenic_region ; MODIFIER	silent_mutation	Average:63.84; most accessible tissue: Minghui63 young leaf, score: 76.385	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412124666	3.65E-06	3.64E-06	mr1347	Jap_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
vg0412124666	9.47E-06	9.48E-06	mr1366	Jap_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
vg0412124666	NA	8.02E-10	mr1714	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