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Detailed information for vg0210303462:

Variant ID: vg0210303462 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10303462
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CGCTGCTAACCTCTTTTTCTAATGGCTTTGTCAGGACGTCCAGAAAAGTGCCGGGCTCGAGTGGTTCTCGTCTGGACGCACGCCGTGCTAGATCATCCGG[C/T]
TCGATGTTGTCCTTGCGGTATACGTGTCGGACCTCGATCCCATCGAACCTTTTCTCCAGCTTCCTGACTTCTGCGAGATAGTTAGATAACTCGGGGTTAG

Reverse complement sequence

CTAACCCCGAGTTATCTAACTATCTCGCAGAAGTCAGGAAGCTGGAGAAAAGGTTCGATGGGATCGAGGTCCGACACGTATACCGCAAGGACAACATCGA[G/A]
CCGGATGATCTAGCACGGCGTGCGTCCAGACGAGAACCACTCGAGCCCGGCACTTTTCTGGACGTCCTGACAAAGCCATTAGAAAAAGAGGTTAGCAGCG

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	63.40%	20.00%	8.89%	7.77%	NA
All Indica	2759	40.10%	33.60%	14.39%	11.96%	NA
All Japonica	1512	98.50%	0.30%	0.40%	0.86%	NA
Aus	269	91.80%	0.40%	1.86%	5.95%	NA
Indica I	595	23.20%	51.90%	13.45%	11.43%	NA
Indica II	465	34.60%	26.50%	19.14%	19.78%	NA
Indica III	913	55.10%	23.20%	13.03%	8.65%	NA
Indica Intermediate	786	38.70%	35.90%	13.87%	11.58%	NA
Temperate Japonica	767	98.70%	0.10%	0.26%	0.91%	NA
Tropical Japonica	504	97.80%	0.40%	0.60%	1.19%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	0.00%	5.21%	0.00%	NA
Intermediate	90	70.00%	13.30%	7.78%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210303462	C -> T	LOC_Os02g17820.1	synonymous_variant ; p.Glu1261Glu; LOW	synonymous_codon	Average:32.564; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg0210303462	C -> DEL	LOC_Os02g17820.1	N	frameshift_variant	Average:32.564; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210303462	7.74E-06	5.52E-08	mr1371_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
vg0210303462	NA	4.87E-06	mr1371_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
vg0210303462	NA	1.14E-06	mr1655_2	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