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Detailed information for vg0808034898:

Variant ID: vg0808034898 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8034898
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

GCAACGCAGCTACACCACTCGTCCAAGCCATGTTCTTCAATAACAATGGCCTGAGTTCATTTGATGCTGCCGAGATCTTCGACAAGCTAAGAATTGCTCC[G/A]
GATACATATTTTAATAATATCAAGGAAGCTGGAAGAATGGGAGCAGGCCTGGCATTGGCGATGACCAAGTCCTTGTACCCGAAGATTGATATTGACGCCA

Reverse complement sequence

TGGCGTCAATATCAATCTTCGGGTACAAGGACTTGGTCATCGCCAATGCCAGGCCTGCTCCCATTCTTCCAGCTTCCTTGATATTATTAAAATATGTATC[C/T]
GGAGCAATTCTTAGCTTGTCGAAGATCTCGGCAGCATCAAATGAACTCAGGCCATTGTTATTGAAGAACATGGCTTGGACGAGTGGTGTAGCTGCGTTGC

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	57.20%	40.50%	0.17%	2.09%	NA
All Indica	2759	82.60%	17.20%	0.18%	0.00%	NA
All Japonica	1512	11.10%	82.30%	0.13%	6.48%	NA
Aus	269	48.00%	52.00%	0.00%	0.00%	NA
Indica I	595	92.60%	7.40%	0.00%	0.00%	NA
Indica II	465	53.80%	45.40%	0.86%	0.00%	NA
Indica III	913	88.10%	11.90%	0.00%	0.00%	NA
Indica Intermediate	786	85.80%	14.10%	0.13%	0.00%	NA
Temperate Japonica	767	3.00%	94.00%	0.00%	3.00%	NA
Tropical Japonica	504	21.40%	75.80%	0.00%	2.78%	NA
Japonica Intermediate	241	15.40%	58.50%	0.83%	25.31%	NA
VI/Aromatic	96	77.10%	22.90%	0.00%	0.00%	NA
Intermediate	90	61.10%	36.70%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808034898	G -> A	LOC_Os08g13500.1	synonymous_variant ; p.Pro638Pro; LOW	synonymous_codon	Average:43.54; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg0808034898	G -> DEL	LOC_Os08g13500.1	N	frameshift_variant	Average:43.54; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808034898	5.29E-06	NA	mr1480_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
vg0808034898	NA	6.28E-06	mr1863_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
vg0808034898	5.85E-06	5.65E-21	mr1968_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
vg0808034898	4.81E-06	8.73E-08	mr1968_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