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Detailed information for vg0521689430:

Variant ID: vg0521689430 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 21689430
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.04, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CAAACCAGGGATTTCCGGTTAGAAATAACCCCATTTTTGACAAGGTCATTCAAATGCTTGTCTTTGATGGCCGAAGGGCCTAAAAGAATAGCACTTTTCT[C/T]
GGATTTTTTGACCTTTTTTGACTTGCCCTTTTTGGTTGTTTTTTGCTTATCTTTCCCCATCACGAAGAAAAGTGAAACGTCGAGCGAAAAGGGTGTTTTC

Reverse complement sequence

GAAAACACCCTTTTCGCTCGACGTTTCACTTTTCTTCGTGATGGGGAAAGATAAGCAAAAAACAACCAAAAAGGGCAAGTCAAAAAAGGTCAAAAAATCC[G/A]
AGAAAAGTGCTATTCTTTTAGGCCCTTCGGCCATCAAAGACAAGCATTTGAATGACCTTGTCAAAAATGGGGTTATTTCTAACCGGAAATCCCTGGTTTG

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	64.60%	35.10%	0.28%	0.02%	NA
All Indica	2759	98.30%	1.40%	0.22%	0.04%	NA
All Japonica	1512	6.30%	93.30%	0.40%	0.00%	NA
Aus	269	70.30%	29.70%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	96.80%	3.00%	0.22%	0.00%	NA
Indica III	913	99.50%	0.30%	0.11%	0.11%	NA
Indica Intermediate	786	96.90%	2.50%	0.51%	0.00%	NA
Temperate Japonica	767	1.20%	98.70%	0.13%	0.00%	NA
Tropical Japonica	504	16.70%	82.70%	0.60%	0.00%	NA
Japonica Intermediate	241	0.80%	98.30%	0.83%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	58.90%	40.00%	1.11%	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
vg0521689430	C -> T	LOC_Os05g37100.1	missense_variant ; p.Glu21Lys; MODERATE	nonsynonymous_codon ; E21K	Average:38.369; most accessible tissue: Callus, score: 66.992	unknown	unknown	DELETERIOUS	0.00
vg0521689430	C -> DEL	LOC_Os05g37100.1	N	frameshift_variant	Average:38.369; most accessible tissue: Callus, score: 66.992	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0521689430	NA	9.57E-66	mr1027	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
vg0521689430	NA	2.50E-16	mr1218	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
vg0521689430	NA	8.79E-32	mr1448	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
vg0521689430	NA	3.61E-07	mr1622	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
vg0521689430	NA	4.55E-66	mr1125_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
vg0521689430	NA	1.33E-07	mr1125_2	Jap_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
vg0521689430	NA	7.29E-08	mr1188_2	Jap_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
vg0521689430	8.53E-06	3.68E-20	mr1218_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
vg0521689430	9.73E-07	6.41E-09	mr1218_2	Jap_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
vg0521689430	NA	3.37E-07	mr1446_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