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Detailed information for vg0102255943:

Variant ID: vg0102255943 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2255943
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTATTTTATGCGTACTTATGCTTTTTAGTTTTTTTTTTAAAAATAAATAAGACGAACAATCAAAGTTGGACACGAAAACTTATGGCTGAGTTTATTCTG[G/A]
GACAGATAAAGTATTTCAGATAGGTCTGCATGTATCTCTTACGGCACTGAGCCTTTTTATATCTATGTGCCACATCTTTTGTTTTTGTTTTAGTTATTAT

Reverse complement sequence

ATAATAACTAAAACAAAAACAAAAGATGTGGCACATAGATATAAAAAGGCTCAGTGCCGTAAGAGATACATGCAGACCTATCTGAAATACTTTATCTGTC[C/T]
CAGAATAAACTCAGCCATAAGTTTTCGTGTCCAACTTTGATTGTTCGTCTTATTTATTTTTAAAAAAAAAACTAAAAAGCATAAGTACGCATAAAATACT

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	74.10%	0.50%	18.45%	6.94%	NA
All Indica	2759	62.40%	0.70%	26.46%	10.44%	NA
All Japonica	1512	88.80%	0.30%	8.53%	2.45%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	41.20%	0.70%	48.57%	9.58%	NA
Indica II	465	67.30%	0.40%	25.81%	6.45%	NA
Indica III	913	72.30%	0.90%	11.83%	15.01%	NA
Indica Intermediate	786	64.10%	0.60%	27.10%	8.14%	NA
Temperate Japonica	767	91.00%	0.00%	7.56%	1.43%	NA
Tropical Japonica	504	89.10%	0.60%	7.34%	2.98%	NA
Japonica Intermediate	241	80.90%	0.40%	14.11%	4.56%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	87.80%	0.00%	10.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0102255943	G -> A	LOC_Os01g04870.1	upstream_gene_variant ; 870.0bp to feature; MODIFIER	silent_mutation	Average:42.352; most accessible tissue: Callus, score: 72.189	N	N	N	N
vg0102255943	G -> A	LOC_Os01g04870-LOC_Os01g04880	intergenic_region ; MODIFIER	silent_mutation	Average:42.352; most accessible tissue: Callus, score: 72.189	N	N	N	N
vg0102255943	G -> DEL	N	N	silent_mutation	Average:42.352; most accessible tissue: Callus, score: 72.189	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102255943	3.06E-06	3.06E-06	mr1655	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
vg0102255943	1.07E-06	1.07E-06	mr1872	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