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Detailed information for vg0507579091:

Variant ID: vg0507579091 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7579091
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.17, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GGTTTTTGTCGGTATCGGCTAAATTGTTTTACTATATTAGATTAGCTAAGGCATCTACCACCCTAAAAATCAGTCCAGGGCTTGATTGTCTAGATATTAT[A/G]
TTTCTTTTTATACTTAGTGCTGCATCAGTTAAGTTTGATCTACTAAGTTGTGTTTAGAACCATATTCTCTAGCCTGCTTCTTGATTGCCAATAAGGATTT

Reverse complement sequence

AAATCCTTATTGGCAATCAAGAAGCAGGCTAGAGAATATGGTTCTAAACACAACTTAGTAGATCAAACTTAACTGATGCAGCACTAAGTATAAAAAGAAA[T/C]
ATAATATCTAGACAATCAAGCCCTGGACTGATTTTTAGGGTGGTAGATGCCTTAGCTAATCTAATATAGTAAAACAATTTAGCCGATACCGACAAAAACC

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	44.90%	12.00%	1.33%	41.81%	NA
All Indica	2759	23.00%	5.90%	2.25%	68.90%	NA
All Japonica	1512	90.30%	8.70%	0.00%	0.99%	NA
Aus	269	19.30%	66.50%	0.37%	13.75%	NA
Indica I	595	19.20%	0.30%	2.18%	78.32%	NA
Indica II	465	32.50%	2.80%	1.29%	63.44%	NA
Indica III	913	20.90%	6.70%	0.99%	71.41%	NA
Indica Intermediate	786	22.60%	10.90%	4.33%	62.09%	NA
Temperate Japonica	767	97.80%	0.80%	0.00%	1.43%	NA
Tropical Japonica	504	79.00%	20.40%	0.00%	0.60%	NA
Japonica Intermediate	241	90.00%	9.50%	0.00%	0.41%	NA
VI/Aromatic	96	22.90%	77.10%	0.00%	0.00%	NA
Intermediate	90	53.30%	21.10%	0.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507579091	A -> DEL	N	N	silent_mutation	Average:9.708; most accessible tissue: Callus, score: 22.696	N	N	N	N
vg0507579091	A -> G	LOC_Os05g13680.1	upstream_gene_variant ; 1405.0bp to feature; MODIFIER	silent_mutation	Average:9.708; most accessible tissue: Callus, score: 22.696	N	N	N	N
vg0507579091	A -> G	LOC_Os05g13670-LOC_Os05g13680	intergenic_region ; MODIFIER	silent_mutation	Average:9.708; most accessible tissue: Callus, score: 22.696	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507579091	NA	8.21E-08	mr1942	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
vg0507579091	9.98E-06	3.23E-07	mr1047_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
vg0507579091	NA	3.04E-08	mr1126_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
vg0507579091	5.39E-08	1.62E-10	mr1530_2	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
vg0507579091	NA	4.83E-07	mr1567_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
vg0507579091	NA	2.35E-08	mr1642_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