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Detailed information for vg0136012918:

Variant ID: vg0136012918 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 36012918
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGCTGGCAGGATGTGTCAATGATCAGAAGGGAAATTAAAGAAAAGGGACTGAAGAGGATCACTGGTTGCAGTTGGATTGAGGTCCAGAACCAGGTTCA[T/C]
GTCTTCTTCAATGGAGACCGCAGACATCCAAAGAGTGATGATATTTACATGATGCTTGAATCTTGTCTGAATAGCGAGGAAGATGAGGACTGCCTTGTAT

Reverse complement sequence

ATACAAGGCAGTCCTCATCTTCCTCGCTATTCAGACAAGATTCAAGCATCATGTAAATATCATCACTCTTTGGATGTCTGCGGTCTCCATTGAAGAAGAC[A/G]
TGAACCTGGTTCTGGACCTCAATCCAACTGCAACCAGTGATCCTCTTCAGTCCCTTTTCTTTAATTTCCCTTCTGATCATTGACACATCCTGCCAGCTTC

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	97.90%	2.10%	0.02%	0.00%	NA
All Indica	2759	96.60%	3.40%	0.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.90%	9.10%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	2.90%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0136012918	T -> C	LOC_Os01g62220.1	synonymous_variant ; p.His423His; LOW	synonymous_codon	Average:63.678; most accessible tissue: Callus, score: 75.215	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0136012918	NA	7.50E-06	mr1457_2	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
vg0136012918	NA	7.00E-08	mr1458_2	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