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Detailed information for vg0226200932:

Variant ID: vg0226200932 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 26200932
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGCTCTCCCACGAGCATGGACCTCGGCGATGTCAAGGTGAGATGTCCCGTCTTGAGATCGTGCATCAGATCGGCAGAGACGAGCACCAGCTGCTTCAC[C/T]
AGGGTGCCAACCACAAGGCCGGCTATGACGCCATTGTCCTTGCCAGCCCAAGCTGCAAAGACGAAGAGAGCGATCTTGCCGTAGTTGTACCCCATGTTGA

Reverse complement sequence

TCAACATGGGGTACAACTACGGCAAGATCGCTCTCTTCGTCTTTGCAGCTTGGGCTGGCAAGGACAATGGCGTCATAGCCGGCCTTGTGGTTGGCACCCT[G/A]
GTGAAGCAGCTGGTGCTCGTCTCTGCCGATCTGATGCACGATCTCAAGACGGGACATCTCACCTTGACATCGCCGAGGTCCATGCTCGTGGGAGAGCTCA

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	97.30%	2.70%	0.02%	0.00%	NA
All Indica	2759	95.40%	4.60%	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	93.60%	6.40%	0.00%	0.00%	NA
Indica II	465	96.30%	3.70%	0.00%	0.00%	NA
Indica III	913	95.70%	4.30%	0.00%	0.00%	NA
Indica Intermediate	786	95.80%	4.10%	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	97.80%	2.20%	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
vg0226200932	C -> T	LOC_Os02g43410.1	synonymous_variant ; p.Leu474Leu; LOW	synonymous_codon	Average:73.286; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N
vg0226200932	C -> T	LOC_Os02g43410.2	synonymous_variant ; p.Leu106Leu; LOW	synonymous_codon	Average:73.286; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0226200932	8.29E-07	6.93E-06	mr1548	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