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Detailed information for vg0106797241:

Variant ID: vg0106797241 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 6797241
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

CATTATGGTCACTGAAATTATGATCACCGAAGTAGCGAAGTATTTGAAAGACAGGAAAAAAATGAAGTTGGAAATATTCTGTTCCACTTCCCAGAAAATA[G/A]
TTTACTTGAACTGATGCTTGTTAGAAAAAAATGCTGATATGCAGATCACTTCCCATGCAGCTACATAGCTCAAGAACGTGCACATCGTATTACATATTTG

Reverse complement sequence

CAAATATGTAATACGATGTGCACGTTCTTGAGCTATGTAGCTGCATGGGAAGTGATCTGCATATCAGCATTTTTTTCTAACAAGCATCAGTTCAAGTAAA[C/T]
TATTTTCTGGGAAGTGGAACAGAATATTTCCAACTTCATTTTTTTCCTGTCTTTCAAATACTTCGCTACTTCGGTGATCATAATTTCAGTGACCATAATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.90%	8.00%	0.08%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	75.10%	24.60%	0.26%	0.00%	NA
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	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	67.80%	31.70%	0.52%	0.00%	NA
Tropical Japonica	504	79.40%	20.60%	0.00%	0.00%	NA
Japonica Intermediate	241	89.60%	10.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0106797241	G -> A	LOC_Os01g12430.1	upstream_gene_variant ; 3895.0bp to feature; MODIFIER	silent_mutation	Average:51.553; most accessible tissue: Callus, score: 92.866	N	N	N	N
vg0106797241	G -> A	LOC_Os01g12430-LOC_Os01g12440	intergenic_region ; MODIFIER	silent_mutation	Average:51.553; most accessible tissue: Callus, score: 92.866	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0106797241	1.39E-07	NA	mr1676_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