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Detailed information for vg0909238381:

Variant ID: vg0909238381 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9238381
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAGTTTCTCATGCTTATGTGATTCCTGAAGCTATTAATACTGCTGCTGAAAAAACTGCTTTTGAACAAAATTGCAAAGCTCGCAACATTCTTTTGAGC[G/T]
GTATTTCTCGTTCGGATTATGATCGTGTTGCTCATCTTCAAACTGCTCATGAGATTTGGGTTGCTTTGAGTAATTTTCATCAAGGAACAAATAACATTAA

Reverse complement sequence

TTAATGTTATTTGTTCCTTGATGAAAATTACTCAAAGCAACCCAAATCTCATGAGCAGTTTGAAGATGAGCAACACGATCATAATCCGAACGAGAAATAC[C/A]
GCTCAAAAGAATGTTGCGAGCTTTGCAATTTTGTTCAAAAGCAGTTTTTTCAGCAGCAGTATTAATAGCTTCAGGAATCACATAAGCATGAGAAACTTTT

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	94.20%	4.60%	1.25%	0.00%	NA
All Indica	2759	96.20%	3.30%	0.47%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	39.40%	44.20%	16.36%	0.00%	NA
Indica I	595	95.80%	4.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	97.30%	2.70%	0.00%	0.00%	NA
Indica Intermediate	786	93.10%	5.20%	1.65%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	2.22%	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
vg0909238381	G -> T	LOC_Os09g15220.1	missense_variant ; p.Gly73Cys; MODERATE	nonsynonymous_codon ; G73C	Average:15.839; most accessible tissue: Zhenshan97 flag leaf, score: 21.748	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909238381	NA	8.29E-06	mr1344_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
vg0909238381	3.16E-09	NA	mr1550_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