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Detailed information for vg0207123792:

Variant ID: vg0207123792 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7123792
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.02, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TTATGTGATTTGTATATTTCCCAGATCTATTTAAGACGCATAGGTCTCTTAGGATTGCCACAACTTCAAGTTCAGCGAGTGAAAACCAATGGCATTTGTT[T/G]
TGCCCTCATCATATTCAAAGAGCTATCTTTCTTTGCCTCATCCGAGGATTTCAAGTACAAAACAAGTTAGTTTTGGCATAGCAGCAGGTGATGACGTGTG

Reverse complement sequence

CACACGTCATCACCTGCTGCTATGCCAAAACTAACTTGTTTTGTACTTGAAATCCTCGGATGAGGCAAAGAAAGATAGCTCTTTGAATATGATGAGGGCA[A/C]
AACAAATGCCATTGGTTTTCACTCGCTGAACTTGAAGTTGTGGCAATCCTAAGAGACCTATGCGTCTTAAATAGATCTGGGAAATATACAAATCACATAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.00%	34.70%	0.13%	0.11%	NA
All Indica	2759	53.20%	46.50%	0.14%	0.18%	NA
All Japonica	1512	95.20%	4.70%	0.07%	0.00%	NA
Aus	269	32.70%	67.30%	0.00%	0.00%	NA
Indica I	595	60.50%	39.00%	0.17%	0.34%	NA
Indica II	465	33.80%	65.80%	0.43%	0.00%	NA
Indica III	913	65.00%	34.80%	0.00%	0.22%	NA
Indica Intermediate	786	45.40%	54.30%	0.13%	0.13%	NA
Temperate Japonica	767	93.60%	6.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.40%	0.20%	0.00%	NA
Japonica Intermediate	241	93.80%	6.20%	0.00%	0.00%	NA
VI/Aromatic	96	33.30%	65.60%	1.04%	0.00%	NA
Intermediate	90	51.10%	48.90%	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
vg0207123792	T -> G	LOC_Os02g13350.1	missense_variant ; p.Leu5Val; MODERATE	nonsynonymous_codon ; L5V	Average:47.84; most accessible tissue: Callus, score: 82.773	unknown	unknown	TOLERATED	1.00
vg0207123792	T -> DEL	LOC_Os02g13350.1	N	frameshift_variant	Average:47.84; most accessible tissue: Callus, score: 82.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207123792	NA	2.98E-06	mr1072	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
vg0207123792	NA	6.68E-07	mr1077	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
vg0207123792	NA	5.24E-06	mr1347	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
vg0207123792	NA	2.46E-07	mr1619	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
vg0207123792	2.26E-06	NA	mr1717	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
vg0207123792	2.95E-08	2.95E-08	mr1717	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