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Detailed information for vg0810981948:

Variant ID: vg0810981948 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10981948
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAGTGGGAGGAAATCGGTATGGATTTCATCACTGGTCTACCCAGAACGGCATCAGGCCATGACTCTATTTGGGTGATAGTCGACAGACTTACCAAAGT[A/G]
GCTCATTTCATCCTAGTAAAGACAACATATTCCGGAAGTCGGTTGGCGGAATTGTATATGGCAAGGATTGTGTGTTTGCATGGCGTCCCTAAGAAAATAG

Reverse complement sequence

CTATTTTCTTAGGGACGCCATGCAAACACACAATCCTTGCCATATACAATTCCGCCAACCGACTTCCGGAATATGTTGTCTTTACTAGGATGAAATGAGC[T/C]
ACTTTGGTAAGTCTGTCGACTATCACCCAAATAGAGTCATGGCCTGATGCCGTTCTGGGTAGACCAGTGATGAAATCCATACCGATTTCCTCCCACTTCC

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	43.30%	14.20%	17.05%	25.37%	NA
All Indica	2759	17.30%	23.50%	23.12%	36.14%	NA
All Japonica	1512	93.80%	0.00%	0.60%	5.56%	NA
Aus	269	2.60%	8.20%	53.53%	35.69%	NA
Indica I	595	5.00%	21.00%	21.85%	52.10%	NA
Indica II	465	12.00%	9.20%	27.10%	51.61%	NA
Indica III	913	30.70%	38.30%	17.85%	13.14%	NA
Indica Intermediate	786	14.00%	16.50%	27.86%	41.60%	NA
Temperate Japonica	767	95.30%	0.00%	0.65%	4.04%	NA
Tropical Japonica	504	94.20%	0.00%	0.00%	5.75%	NA
Japonica Intermediate	241	88.40%	0.00%	1.66%	9.96%	NA
VI/Aromatic	96	94.80%	0.00%	3.12%	2.08%	NA
Intermediate	90	61.10%	3.30%	13.33%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0810981948	A -> G	LOC_Os08g17890.1	synonymous_variant ; p.Val1163Val; LOW	synonymous_codon	Average:15.207; most accessible tissue: Minghui63 young leaf, score: 22.423	N	N	N	N
vg0810981948	A -> DEL	LOC_Os08g17890.1	N	frameshift_variant	Average:15.207; most accessible tissue: Minghui63 young leaf, score: 22.423	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810981948	NA	8.02E-06	mr1715	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