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Detailed information for vg0825594684:

Variant ID: vg0825594684 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25594684
Reference Allele: G	Alternative Allele: T,A
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCTTTCTGTTCTGATAAGGAGATGAAACTATCAATTTCATTCTTTTTTAGGGCAAGTGCTTGAGCCTCTGAGTCCATTTTAGTTTGTGCTTCCTGAAGG[G/T,A]
TTTTGAGCTTTAGATCAATATCTGTCTGGGATCCATAAAATCTGGAGACAACGGCAGTGATCCTTTCTTGAACCTCCTGGATCTGAGCATTGTTTTCAGC

Reverse complement sequence

GCTGAAAACAATGCTCAGATCCAGGAGGTTCAAGAAAGGATCACTGCCGTTGTCTCCAGATTTTATGGATCCCAGACAGATATTGATCTAAAGCTCAAAA[C/A,T]
CCTTCAGGAAGCACAAACTAAAATGGACTCAGAGGCTCAAGCACTTGCCCTAAAAAAGAATGAAATTGATAGTTTCATCTCCTTATCAGAACAGAAAGAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.40%	0.70%	0.91%	0.00%	A: 0.02%
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	95.00%	2.10%	2.78%	0.00%	A: 0.07%
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	90.60%	4.00%	5.35%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.00%	A: 0.20%
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	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
vg0825594684	G -> T	LOC_Os08g40450.1	missense_variant ; p.Thr497Asn; MODERATE	nonsynonymous_codon ; T497N	Average:46.587; most accessible tissue: Callus, score: 74.801	unknown	unknown	TOLERATED	0.80
vg0825594684	G -> A	LOC_Os08g40450.1	missense_variant ; p.Thr497Ile; MODERATE	nonsynonymous_codon ; T497I	Average:46.587; most accessible tissue: Callus, score: 74.801	unknown	unknown	TOLERATED	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825594684	NA	1.98E-06	mr1069	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
vg0825594684	5.37E-06	NA	mr1101	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
vg0825594684	1.40E-06	7.94E-06	mr1150	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