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Detailed information for vg0100401934:

Variant ID: vg0100401934 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 401934
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TTGAAAAAAATCCGCACTAGTATTATTGGTGCTGGTCTTTATATTAGAACCGGTGTCTATAGTTGCTCAAAGGTGTCAGTTTTTTTTTTATCCCATAGAA[A/G]
CGAAAAAGGTTAATAGATATCGATTTTAAATGAACCGACAACCATGAGTCGGTACCTACGGAGGATTTTATAGTAATGGTCCGTACTTTTATTTCAGATT

Reverse complement sequence

AATCTGAAATAAAAGTACGGACCATTACTATAAAATCCTCCGTAGGTACCGACTCATGGTTGTCGGTTCATTTAAAATCGATATCTATTAACCTTTTTCG[T/C]
TTCTATGGGATAAAAAAAAAACTGACACCTTTGAGCAACTATAGACACCGGTTCTAATATAAAGACCAGCACCAATAATACTAGTGCGGATTTTTTTCAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.90%	49.80%	0.30%	0.08%	NA
All Indica	2759	29.50%	70.00%	0.29%	0.14%	NA
All Japonica	1512	89.50%	10.30%	0.26%	0.00%	NA
Aus	269	24.20%	75.80%	0.00%	0.00%	NA
Indica I	595	1.70%	98.20%	0.17%	0.00%	NA
Indica II	465	34.40%	65.40%	0.22%	0.00%	NA
Indica III	913	46.10%	53.70%	0.00%	0.22%	NA
Indica Intermediate	786	28.50%	70.50%	0.76%	0.25%	NA
Temperate Japonica	767	86.40%	13.20%	0.39%	0.00%	NA
Tropical Japonica	504	91.70%	8.10%	0.20%	0.00%	NA
Japonica Intermediate	241	94.60%	5.40%	0.00%	0.00%	NA
VI/Aromatic	96	74.00%	26.00%	0.00%	0.00%	NA
Intermediate	90	57.80%	40.00%	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
vg0100401934	A -> G	LOC_Os01g01760.1	downstream_gene_variant ; 1758.0bp to feature; MODIFIER	silent_mutation	Average:51.202; most accessible tissue: Callus, score: 72.608	N	N	N	N
vg0100401934	A -> G	LOC_Os01g01740-LOC_Os01g01760	intergenic_region ; MODIFIER	silent_mutation	Average:51.202; most accessible tissue: Callus, score: 72.608	N	N	N	N
vg0100401934	A -> DEL	N	N	silent_mutation	Average:51.202; most accessible tissue: Callus, score: 72.608	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0100401934	4.59E-06	1.20E-06	mr1870	Ind_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