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Detailed information for vg0103495750:

Variant ID: vg0103495750 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3495750
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TTAAGCTCAAGGCGGGTGGTAGTTCAGACAAAGTGGCATATTTCAGGATAATAAAGTGTCGACATATTTAGCATGGTAAGTGCTACATTGAGGTATGCTG[G/A]
CGGTTCATATGATCAGCAAAAAATGTATTGCTTGATATAAACATCAAGATGAAGTTCCAGAATTCGAGAAGCGGTGCATACAATTAAGCATTAGACAGTC

Reverse complement sequence

GACTGTCTAATGCTTAATTGTATGCACCGCTTCTCGAATTCTGGAACTTCATCTTGATGTTTATATCAAGCAATACATTTTTTGCTGATCATATGAACCG[C/T]
CAGCATACCTCAATGTAGCACTTACCATGCTAAATATGTCGACACTTTATTATCCTGAAATATGCCACTTTGTCTGAACTACCACCCGCCTTGAGCTTAA

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	74.60%	25.30%	0.08%	0.00%	NA
All Indica	2759	63.30%	36.60%	0.11%	0.00%	NA
All Japonica	1512	90.40%	9.60%	0.00%	0.00%	NA
Aus	269	96.70%	3.00%	0.37%	0.00%	NA
Indica I	595	65.40%	34.60%	0.00%	0.00%	NA
Indica II	465	65.80%	34.00%	0.22%	0.00%	NA
Indica III	913	65.70%	34.30%	0.00%	0.00%	NA
Indica Intermediate	786	57.50%	42.20%	0.25%	0.00%	NA
Temperate Japonica	767	84.70%	15.30%	0.00%	0.00%	NA
Tropical Japonica	504	96.40%	3.60%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	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
vg0103495750	G -> A	LOC_Os01g07376.1	upstream_gene_variant ; 3759.0bp to feature; MODIFIER	silent_mutation	Average:66.109; most accessible tissue: Zhenshan97 flower, score: 80.006	N	N	N	N
vg0103495750	G -> A	LOC_Os01g07382.1	intron_variant ; MODIFIER	silent_mutation	Average:66.109; most accessible tissue: Zhenshan97 flower, score: 80.006	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103495750	2.91E-06	NA	mr1937	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