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Detailed information for vg0105850195:

Variant ID: vg0105850195 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5850195
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACTTTCAACTTAAATTTGAAAACATTCAACTTTTCATCTCAGCTTTTAAAAACTTTCAACTGAAATTTGAAACATTCAACTCAAATTTGAAAACTTTCA[G/A]
CTCAAAATACAAAAACTTTTAACTCGGATTTGAAAATTTTCAAATCAATATTTTTGAAAAACTTTCAAATCGTATTTTGAAAATTTACAAAATCAATTGT

Reverse complement sequence

ACAATTGATTTTGTAAATTTTCAAAATACGATTTGAAAGTTTTTCAAAAATATTGATTTGAAAATTTTCAAATCCGAGTTAAAAGTTTTTGTATTTTGAG[C/T]
TGAAAGTTTTCAAATTTGAGTTGAATGTTTCAAATTTCAGTTGAAAGTTTTTAAAAGCTGAGATGAAAAGTTGAATGTTTTCAAATTTAAGTTGAAAGTT

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	97.80%	1.20%	1.04%	0.00%	NA
All Indica	2759	99.80%	0.00%	0.18%	0.00%	NA
All Japonica	1512	93.50%	3.70%	2.84%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	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	99.60%	0.00%	0.38%	0.00%	NA
Temperate Japonica	767	89.70%	5.90%	4.43%	0.00%	NA
Tropical Japonica	504	98.80%	0.60%	0.60%	0.00%	NA
Japonica Intermediate	241	94.20%	3.30%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0105850195	G -> A	LOC_Os01g10970.1	downstream_gene_variant ; 1250.0bp to feature; MODIFIER	silent_mutation	Average:17.366; most accessible tissue: Callus, score: 38.046	N	N	N	N
vg0105850195	G -> A	LOC_Os01g10970-LOC_Os01g10980	intergenic_region ; MODIFIER	silent_mutation	Average:17.366; most accessible tissue: Callus, score: 38.046	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105850195	1.20E-06	1.20E-06	mr1038	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
vg0105850195	NA	7.45E-07	mr1549_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