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Detailed information for vg0432418113:

Variant ID: vg0432418113 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32418113
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGTGTCAGCACTGACCAGTGTTGTTAACGATGACATTAAACCACTCAACAGGTCTAGTGGCTCTGAACTGAAGACTCAATGGCAACCAGATTCTAAGA[C/T]
TGATGCTTCCGTTCTGAAGATCTCTAAAGTCGAGACAAGCCTGCAGTTTGATGACAAAGCTAGGGATGGTTATGATGGAGATGAACATGAATGCACAGCC

Reverse complement sequence

GGCTGTGCATTCATGTTCATCTCCATCATAACCATCCCTAGCTTTGTCATCAAACTGCAGGCTTGTCTCGACTTTAGAGATCTTCAGAACGGAAGCATCA[G/A]
TCTTAGAATCTGGTTGCCATTGAGTCTTCAGTTCAGAGCCACTAGACCTGTTGAGTGGTTTAATGTCATCGTTAACAACACTGGTCAGTGCTGACACAGC

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	59.60%	40.20%	0.04%	0.21%	NA
All Indica	2759	75.60%	24.10%	0.00%	0.29%	NA
All Japonica	1512	25.60%	74.20%	0.07%	0.13%	NA
Aus	269	80.70%	19.30%	0.00%	0.00%	NA
Indica I	595	83.70%	15.80%	0.00%	0.50%	NA
Indica II	465	59.60%	40.00%	0.00%	0.43%	NA
Indica III	913	85.90%	14.00%	0.00%	0.11%	NA
Indica Intermediate	786	67.20%	32.60%	0.00%	0.25%	NA
Temperate Japonica	767	23.30%	76.70%	0.00%	0.00%	NA
Tropical Japonica	504	30.40%	69.00%	0.20%	0.40%	NA
Japonica Intermediate	241	22.80%	77.20%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	21.90%	0.00%	0.00%	NA
Intermediate	90	54.40%	44.40%	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
vg0432418113	C -> DEL	N	N	silent_mutation	Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg0432418113	C -> T	LOC_Os04g54500.1	upstream_gene_variant ; 250.0bp to feature; MODIFIER	silent_mutation	Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg0432418113	C -> T	LOC_Os04g54490.1	downstream_gene_variant ; 2500.0bp to feature; MODIFIER	silent_mutation	Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg0432418113	C -> T	LOC_Os04g54490-LOC_Os04g54500	intergenic_region ; MODIFIER	silent_mutation	Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432418113	5.84E-07	6.62E-12	mr1741_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
vg0432418113	NA	1.71E-09	mr1785_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
vg0432418113	2.09E-06	NA	mr1800_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