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Detailed information for vg0611638625:

Variant ID: vg0611638625 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11638625
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.12, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GATATGAGGATAACTACCTGTCTCGTGGGCAAACGGAAGGTTTACGGCACAAACATACAAAGGGGTAATCACACTCTCGCAGCGACGGCAGACGATTTAC[G/A]
GTGCAAATCGACAAAGATGGACTAAAACTAGGGTAAAGTAGAAAGCATGGCTGGCAATTTGAACAAGTGATTCAAGTAGAATGTGTGTTGATTGATTACA

Reverse complement sequence

TGTAATCAATCAACACACATTCTACTTGAATCACTTGTTCAAATTGCCAGCCATGCTTTCTACTTTACCCTAGTTTTAGTCCATCTTTGTCGATTTGCAC[C/T]
GTAAATCGTCTGCCGTCGCTGCGAGAGTGTGATTACCCCTTTGTATGTTTGTGCCGTAAACCTTCCGTTTGCCCACGAGACAGGTAGTTATCCTCATATC

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	94.90%	5.10%	0.00%	0.00%	NA
All Indica	2759	95.80%	4.20%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	80.70%	19.30%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	94.00%	6.00%	0.00%	0.00%	NA
Indica III	913	92.80%	7.20%	0.00%	0.00%	NA
Indica Intermediate	786	97.20%	2.80%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	31.20%	68.80%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0611638625	G -> A	LOC_Os06g20280.1	intron_variant ; MODIFIER	silent_mutation	Average:53.527; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611638625	1.28E-07	NA	mr1695	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
vg0611638625	1.27E-06	NA	mr1695_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