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Detailed information for vg0617626072:

Variant ID: vg0617626072 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17626072
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.04, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGATGAGAGGTGGGCCGCTGATGGTGACAGCTCAGTACGGGTATTCCTCCGCGCCTATATATAATCCTAAGTTAATTTCCTGGGGAGGGTATTCCTCC[A/G]
TATTTAGCCCCGGTTGGATGGTCATGACGGGCTGTCATAAGGAACTCGACAGTCAGGGGTGGCTTCTCGAAGTACCAGGAGGGCATTGGATAGAGGGTAT

Reverse complement sequence

ATACCCTCTATCCAATGCCCTCCTGGTACTTCGAGAAGCCACCCCTGACTGTCGAGTTCCTTATGACAGCCCGTCATGACCATCCAACCGGGGCTAAATA[T/C]
GGAGGAATACCCTCCCCAGGAAATTAACTTAGGATTATATATAGGCGCGGAGGAATACCCGTACTGAGCTGTCACCATCAGCGGCCCACCTCTCATCCGC

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	45.90%	2.20%	13.48%	38.47%	NA
All Indica	2759	20.20%	2.60%	16.35%	60.93%	NA
All Japonica	1512	88.00%	1.70%	8.27%	2.05%	NA
Aus	269	63.20%	1.10%	12.27%	23.42%	NA
Indica I	595	6.20%	1.50%	10.59%	81.68%	NA
Indica II	465	17.00%	0.60%	6.67%	75.70%	NA
Indica III	913	29.80%	5.60%	27.05%	37.57%	NA
Indica Intermediate	786	21.40%	1.00%	13.99%	63.61%	NA
Temperate Japonica	767	93.90%	0.50%	3.26%	2.35%	NA
Tropical Japonica	504	78.40%	4.00%	16.47%	1.19%	NA
Japonica Intermediate	241	89.60%	0.40%	7.05%	2.90%	NA
VI/Aromatic	96	64.60%	3.10%	16.67%	15.62%	NA
Intermediate	90	53.30%	2.20%	13.33%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0617626072	A -> G	LOC_Os06g30490.1	upstream_gene_variant ; 870.0bp to feature; MODIFIER	silent_mutation	Average:14.047; most accessible tissue: Callus, score: 27.076	N	N	N	N
vg0617626072	A -> G	LOC_Os06g30500.1	downstream_gene_variant ; 4500.0bp to feature; MODIFIER	silent_mutation	Average:14.047; most accessible tissue: Callus, score: 27.076	N	N	N	N
vg0617626072	A -> G	LOC_Os06g30480-LOC_Os06g30490	intergenic_region ; MODIFIER	silent_mutation	Average:14.047; most accessible tissue: Callus, score: 27.076	N	N	N	N
vg0617626072	A -> DEL	N	N	silent_mutation	Average:14.047; most accessible tissue: Callus, score: 27.076	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617626072	6.62E-06	NA	mr1401	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