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Detailed information for vg0817494161:

Variant ID: vg0817494161 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17494161
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, A: 0.36, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGAGATTGCTTTGCTTGGGAGTATTATGAGATGCCAGGACTCAGCCGATCAATTGTTGAACATCGGCTTCCTATTAAACCTGGGGTTAGACCATATCA[A/G]
CAGCCACCAAGGAGATGTAAGGCCGATATGCTCGAGGCTATCAAGGCTAAGGTTGCACGTTTGTATGGTGCTGGTTTTATTCGTCCATGCCGATATGCTG

Reverse complement sequence

CAGCATATCGGCATGGACGAATAAAACCAGCACCATACAAACGTGCAACCTTAGCCTTGATAGCCTCGAGCATATCGGCCTTACATCTCCTTGGTGGCTG[T/C]
TGATATGGTCTAACCCCAGGTTTAATAGGAAGCCGATGTTCAACAATTGATCGGCTGAGTCCTGGCATCTCATAATACTCCCAAGCAAAGCAATCTCTGT

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%	18.80%	14.18%	22.13%	NA
All Indica	2759	25.10%	22.50%	19.86%	32.55%	NA
All Japonica	1512	83.30%	5.80%	5.09%	5.82%	NA
Aus	269	7.80%	63.20%	14.13%	14.87%	NA
Indica I	595	28.60%	19.70%	20.67%	31.09%	NA
Indica II	465	23.90%	8.60%	27.96%	39.57%	NA
Indica III	913	19.60%	37.00%	13.80%	29.57%	NA
Indica Intermediate	786	29.60%	15.90%	21.50%	32.95%	NA
Temperate Japonica	767	96.70%	1.70%	0.78%	0.78%	NA
Tropical Japonica	504	60.50%	10.90%	13.49%	15.08%	NA
Japonica Intermediate	241	88.00%	8.30%	1.24%	2.49%	NA
VI/Aromatic	96	96.90%	1.00%	1.04%	1.04%	NA
Intermediate	90	60.00%	12.20%	6.67%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817494161	A -> G	LOC_Os08g28630.1	synonymous_variant ; p.Gln781Gln; LOW	stop_gained	Average:10.66; most accessible tissue: Callus, score: 27.14	N	N	N	N
vg0817494161	A -> DEL	LOC_Os08g28630.1	N	frameshift_variant	Average:10.66; most accessible tissue: Callus, score: 27.14	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817494161	3.36E-06	1.49E-07	mr1167_2	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