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Detailed information for vg0434331233:

Variant ID: vg0434331233 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 34331233
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTGAAGCTCTCCGGTAGCTCCCCCTGAAGCTTGTTCCTTGCAAGGTTCAGCGTCCTCAACTCAGTGCACGAGGCAAGGCGAGGCGGTATAGCACCACG[C/T]
AGCGTGTTGGTCCCAGCATCAAAGTTGTTCAGCCTCGTGAGCAATCTGCAGTCAATGGTAATCTCACCGGACAGCGAATTGTTCCTCAGGCTGACCACTC

Reverse complement sequence

GAGTGGTCAGCCTGAGGAACAATTCGCTGTCCGGTGAGATTACCATTGACTGCAGATTGCTCACGAGGCTGAACAACTTTGATGCTGGGACCAACACGCT[G/A]
CGTGGTGCTATACCGCCTCGCCTTGCCTCGTGCACTGAGTTGAGGACGCTGAACCTTGCAAGGAACAAGCTTCAGGGGGAGCTACCGGAGAGCTTCAAGA

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	48.30%	0.20%	1.04%	50.49%	NA
All Indica	2759	13.20%	0.30%	1.74%	84.78%	NA
All Japonica	1512	98.90%	0.10%	0.00%	0.99%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	5.70%	0.00%	3.70%	90.59%	NA
Indica II	465	9.00%	0.40%	1.51%	89.03%	NA
Indica III	913	20.20%	0.20%	0.55%	79.08%	NA
Indica Intermediate	786	13.40%	0.40%	1.78%	84.48%	NA
Temperate Japonica	767	99.60%	0.10%	0.00%	0.26%	NA
Tropical Japonica	504	97.80%	0.00%	0.00%	2.18%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	67.80%	0.00%	1.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0434331233	C -> DEL	LOC_Os04g57660.1	N	frameshift_variant	Average:29.777; most accessible tissue: Zhenshan97 flower, score: 52.901	N	N	N	N
vg0434331233	C -> T	LOC_Os04g57660.1	synonymous_variant ; p.Leu299Leu; LOW	synonymous_codon	Average:29.777; most accessible tissue: Zhenshan97 flower, score: 52.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0434331233	7.02E-06	NA	mr1529	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
vg0434331233	1.05E-06	1.05E-06	mr1529	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