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Detailed information for vg0610639681:

Variant ID: vg0610639681 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10639681
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.76, G: 0.25, others allele: 0.00, population size: 118. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGGACAGTACGGTAGAAATGGTTGATTTCCGGGTGGCTAGTACTGTTCCAACCGACATAAAACTGCCAAGTACATGTGAAGAACATACGAGTACGACC[A/G]
CAATTCTCGTATGGGCATAGACCTAGCTGATTAAGTTATCTAGCAAAGGTGGTACCTCTGTATAGTGGTTCTTCTTAAGTCCTCGCGCAGGAGGCAAACT

Reverse complement sequence

AGTTTGCCTCCTGCGCGAGGACTTAAGAAGAACCACTATACAGAGGTACCACCTTTGCTAGATAACTTAATCAGCTAGGTCTATGCCCATACGAGAATTG[T/C]
GGTCGTACTCGTATGTTCTTCACATGTACTTGGCAGTTTTATGTCGGTTGGAACAGTACTAGCCACCCGGAAATCAACCATTTCTACCGTACTGTCCCAA

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	70.90%	23.00%	3.07%	3.07%	NA
All Indica	2759	96.20%	2.40%	1.09%	0.33%	NA
All Japonica	1512	37.20%	52.80%	5.49%	4.56%	NA
Aus	269	19.70%	51.70%	5.58%	23.05%	NA
Indica I	595	93.40%	5.20%	0.84%	0.50%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	97.90%	1.00%	0.99%	0.11%	NA
Indica Intermediate	786	94.50%	2.90%	1.91%	0.64%	NA
Temperate Japonica	767	47.80%	43.40%	2.87%	5.87%	NA
Tropical Japonica	504	28.20%	58.30%	9.92%	3.57%	NA
Japonica Intermediate	241	22.00%	71.00%	4.56%	2.49%	NA
VI/Aromatic	96	13.50%	66.70%	16.67%	3.12%	NA
Intermediate	90	77.80%	18.90%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610639681	A -> G	LOC_Os06g18770.1	downstream_gene_variant ; 1642.0bp to feature; MODIFIER	silent_mutation	Average:17.22; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0610639681	A -> G	LOC_Os06g18750-LOC_Os06g18770	intergenic_region ; MODIFIER	silent_mutation	Average:17.22; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0610639681	A -> DEL	N	N	silent_mutation	Average:17.22; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610639681	8.80E-06	NA	mr1111_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
vg0610639681	4.77E-06	NA	mr1211_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
vg0610639681	1.23E-06	5.16E-08	mr1526_2	Ind_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
vg0610639681	8.07E-07	3.13E-06	mr1929_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