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Detailed information for vg0810013102:

Variant ID: vg0810013102 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10013102
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

CGACATACGAAGCAAAGCAGGTTCTGTGTTCATTGGGGTTGGAGGTCCGTAGAATTCACGCTTGTCCAAACGACTGCATATTGTACCACAAGCAATATGC[G/A]
GACTTGGATGCTTGTCCTGTCTACAAGGCTTCTCGATACAAGCGAAAGAAAAGTGCTGACAAAGGAAAGAAGTCAAAGAGGGGTGGTCCGGGAAAGGTTG

Reverse complement sequence

CAACCTTTCCCGGACCACCCCTCTTTGACTTCTTTCCTTTGTCAGCACTTTTCTTTCGCTTGTATCGAGAAGCCTTGTAGACAGGACAAGCATCCAAGTC[C/T]
GCATATTGCTTGTGGTACAATATGCAGTCGTTTGGACAAGCGTGAATTCTACGGACCTCCAACCCCAATGAACACAGAACCTGCTTTGCTTCGTATGTCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.00%	6.30%	1.74%	7.87%	NA
All Indica	2759	98.70%	0.60%	0.43%	0.25%	NA
All Japonica	1512	54.30%	18.50%	3.64%	23.61%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	98.70%	0.00%	0.43%	0.86%	NA
Indica III	913	98.80%	0.10%	0.88%	0.22%	NA
Indica Intermediate	786	99.20%	0.40%	0.25%	0.13%	NA
Temperate Japonica	767	67.10%	31.30%	0.13%	1.43%	NA
Tropical Japonica	504	41.70%	0.40%	7.14%	50.79%	NA
Japonica Intermediate	241	39.80%	15.40%	7.47%	37.34%	NA
VI/Aromatic	96	80.20%	1.00%	13.54%	5.21%	NA
Intermediate	90	92.20%	3.30%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0810013102	G -> A	LOC_Os08g16380.1	synonymous_variant ; p.Ala155Ala; LOW	synonymous_codon	Average:50.272; most accessible tissue: Minghui63 flag leaf, score: 74.955	N	N	N	N
vg0810013102	G -> DEL	LOC_Os08g16380.1	N	frameshift_variant	Average:50.272; most accessible tissue: Minghui63 flag leaf, score: 74.955	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810013102	1.68E-09	4.08E-10	mr1057_2	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
vg0810013102	8.36E-06	NA	mr1733_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