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Detailed information for vg0626091811:

Variant ID: vg0626091811 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 26091811
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

TATGAAATTAGTTTTTTTTATTCGTATCCAAAAACCTCTTTTGACATCCGGTCAAACATTTGATGTGGCATCCAAAAATTCTCATTTCATGAACTAAACA[G/A]
GGCCTTACAAGGGCGGATCTACCGGCTTGATTCAGAAGCTTTCCTTGCCAATGTGTCAGCCTTGTCGATACCTTGTTCACTAGGGGGAAACTGAAACTTA

Reverse complement sequence

TAAGTTTCAGTTTCCCCCTAGTGAACAAGGTATCGACAAGGCTGACACATTGGCAAGGAAAGCTTCTGAATCAAGCCGGTAGATCCGCCCTTGTAAGGCC[C/T]
TGTTTAGTTCATGAAATGAGAATTTTTGGATGCCACATCAAATGTTTGACCGGATGTCAAAAGAGGTTTTTGGATACGAATAAAAAAAACTAATTTCATA

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	35.70%	29.40%	1.06%	33.83%	NA
All Indica	2759	3.70%	42.90%	1.59%	51.83%	NA
All Japonica	1512	97.70%	1.80%	0.07%	0.46%	NA
Aus	269	2.20%	52.40%	1.86%	43.49%	NA
Indica I	595	1.70%	21.50%	2.69%	74.12%	NA
Indica II	465	6.50%	19.60%	1.94%	72.04%	NA
Indica III	913	0.90%	64.00%	0.88%	34.28%	NA
Indica Intermediate	786	6.70%	48.50%	1.40%	43.38%	NA
Temperate Japonica	767	99.10%	0.30%	0.13%	0.52%	NA
Tropical Japonica	504	94.80%	4.60%	0.00%	0.60%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	62.50%	17.70%	0.00%	19.79%	NA
Intermediate	90	50.00%	21.10%	0.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0626091811	G -> A	LOC_Os06g43410.1	upstream_gene_variant ; 705.0bp to feature; MODIFIER	silent_mutation	Average:30.4; most accessible tissue: Minghui63 root, score: 79.068	N	N	N	N
vg0626091811	G -> A	LOC_Os06g43384.1	downstream_gene_variant ; 4720.0bp to feature; MODIFIER	silent_mutation	Average:30.4; most accessible tissue: Minghui63 root, score: 79.068	N	N	N	N
vg0626091811	G -> A	LOC_Os06g43384-LOC_Os06g43410	intergenic_region ; MODIFIER	silent_mutation	Average:30.4; most accessible tissue: Minghui63 root, score: 79.068	N	N	N	N
vg0626091811	G -> DEL	N	N	silent_mutation	Average:30.4; most accessible tissue: Minghui63 root, score: 79.068	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0626091811	NA	6.96E-07	mr1690	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
vg0626091811	NA	3.44E-09	mr1322_2	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
vg0626091811	NA	3.37E-08	mr1335_2	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
vg0626091811	NA	3.31E-08	mr1623_2	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
vg0626091811	3.74E-06	9.46E-18	mr1686_2	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