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Detailed information for vg1117462451:

Variant ID: vg1117462451 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17462451
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.20, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GTGATATCTCCTAATACCAGTGCTAAAGAATTGTAGAGGTCACGGTCTATCTTGGCTCCGCAGCAATTGTCAAATTTCATAGTATTGGTACCAACAATAA[G/A]
ATGATTTTTCTAATTAAAATTCAAATTAGACCCTCTATATATGTTGGCCGGTTACCTTGACAACCTCAAATATCGTAAATTTTAGAGATCTGCTCCGGTC

Reverse complement sequence

GACCGGAGCAGATCTCTAAAATTTACGATATTTGAGGTTGTCAAGGTAACCGGCCAACATATATAGAGGGTCTAATTTGAATTTTAATTAGAAAAATCAT[C/T]
TTATTGTTGGTACCAATACTATGAAATTTGACAATTGCTGCGGAGCCAAGATAGACCGTGACCTCTACAATTCTTTAGCACTGGTATTAGGAGATATCAC

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	57.90%	39.10%	0.44%	2.50%	NA
All Indica	2759	82.60%	16.80%	0.54%	0.00%	NA
All Japonica	1512	8.60%	83.40%	0.26%	7.74%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	83.50%	16.10%	0.34%	0.00%	NA
Indica II	465	76.80%	23.20%	0.00%	0.00%	NA
Indica III	913	85.20%	14.80%	0.00%	0.00%	NA
Indica Intermediate	786	82.40%	15.90%	1.65%	0.00%	NA
Temperate Japonica	767	2.10%	82.30%	0.52%	15.12%	NA
Tropical Japonica	504	17.90%	81.90%	0.00%	0.20%	NA
Japonica Intermediate	241	10.00%	90.00%	0.00%	0.00%	NA
VI/Aromatic	96	28.10%	71.90%	0.00%	0.00%	NA
Intermediate	90	51.10%	45.60%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117462451	G -> A	LOC_Os11g30020.1	intron_variant ; MODIFIER	silent_mutation	Average:49.395; most accessible tissue: Minghui63 root, score: 64.607	N	N	N	N
vg1117462451	G -> DEL	N	N	silent_mutation	Average:49.395; most accessible tissue: Minghui63 root, score: 64.607	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117462451	3.80E-06	1.07E-06	mr1182	Jap_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
vg1117462451	NA	6.31E-06	mr1282	Jap_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
vg1117462451	3.03E-06	1.46E-06	mr1650	Jap_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
vg1117462451	7.85E-06	3.84E-06	mr1658	Jap_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
vg1117462451	NA	6.10E-07	mr1915_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