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Detailed information for vg0209234819:

Variant ID: vg0209234819 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9234819
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATTTTGCTGTAACTTTTGCTCTCTTGTCTTGATATTGCTTGTTGCGGGTTCCAATTTGTTCACCATTTGTTTTCCAGGCCTGGCAATGTGCTGTACTT[T/C]
CTAGAAATGCAGTACCATTCTCTCTTGGACTTTCACATTGCATGTCTTTAATCAACATAATGTATGCATCTATGACCTGTGAAAGAATAAAGAACAAAAT

Reverse complement sequence

ATTTTGTTCTTTATTCTTTCACAGGTCATAGATGCATACATTATGTTGATTAAAGACATGCAATGTGAAAGTCCAAGAGAGAATGGTACTGCATTTCTAG[A/G]
AAGTACAGCACATTGCCAGGCCTGGAAAACAAATGGTGAACAAATTGGAACCCGCAACAAGCAATATCAAGACAAGAGAGCAAAAGTTACAGCAAAATAT

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	68.30%	2.10%	9.67%	19.93%	NA
All Indica	2759	48.70%	3.40%	15.55%	32.40%	NA
All Japonica	1512	97.90%	0.00%	0.20%	1.92%	NA
Aus	269	88.10%	2.60%	8.92%	0.37%	NA
Indica I	595	49.60%	6.20%	7.56%	36.64%	NA
Indica II	465	57.20%	2.20%	10.54%	30.11%	NA
Indica III	913	39.20%	1.90%	26.40%	32.53%	NA
Indica Intermediate	786	53.90%	3.70%	11.96%	30.41%	NA
Temperate Japonica	767	98.20%	0.00%	0.13%	1.69%	NA
Tropical Japonica	504	97.40%	0.00%	0.40%	2.18%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	77.80%	1.10%	1.11%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0209234819	T -> DEL	LOC_Os02g16240.1	N	frameshift_variant	Average:7.715; most accessible tissue: Callus, score: 33.523	N	N	N	N
vg0209234819	T -> C	LOC_Os02g16240.1	missense_variant ; p.Glu673Gly; MODERATE	nonsynonymous_codon ; E673G	Average:7.715; most accessible tissue: Callus, score: 33.523	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209234819	NA	4.57E-06	mr1795	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
vg0209234819	2.25E-06	NA	mr1962_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
vg0209234819	3.27E-06	NA	mr1962_2	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