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Detailed information for vg0124233988:

Variant ID: vg0124233988 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24233988
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: 245. )

Flanking Sequence (100 bp) in Reference Genome:

CTGAAGGATGAACACCAACCATTTATCTGTGACCATATCAAAATCCTAGTAATTAAAAGCGTCGATTAATCAATGCCCACACTAAAATTCTAACAAAAAC[G/A]
GATCTGTATATATATAATTATGGATAAGTGCACCATACTCCTTTCGTCCTATTTTCATCATCACCTAAGCAAATAGCGTAGAGACCAAGGACAACTAAAC

Reverse complement sequence

GTTTAGTTGTCCTTGGTCTCTACGCTATTTGCTTAGGTGATGATGAAAATAGGACGAAAGGAGTATGGTGCACTTATCCATAATTATATATATACAGATC[C/T]
GTTTTTGTTAGAATTTTAGTGTGGGCATTGATTAATCGACGCTTTTAATTACTAGGATTTTGATATGGTCACAGATAAATGGTTGGTGTTCATCCTTCAG

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	98.90%	0.60%	0.49%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	96.70%	1.80%	1.52%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	93.90%	3.50%	2.61%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0124233988	G -> A	LOC_Os01g42610.1	upstream_gene_variant ; 641.0bp to feature; MODIFIER	silent_mutation	Average:58.531; most accessible tissue: Callus, score: 76.336	N	N	N	N
vg0124233988	G -> A	LOC_Os01g42600.1	downstream_gene_variant ; 3835.0bp to feature; MODIFIER	silent_mutation	Average:58.531; most accessible tissue: Callus, score: 76.336	N	N	N	N
vg0124233988	G -> A	LOC_Os01g42600-LOC_Os01g42610	intergenic_region ; MODIFIER	silent_mutation	Average:58.531; most accessible tissue: Callus, score: 76.336	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124233988	1.69E-06	1.69E-06	mr1456	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
vg0124233988	NA	8.09E-06	mr1932_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