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Detailed information for vg0711196263:

Variant ID: vg0711196263 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11196263
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, A: 0.07, T: 0.04, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTCTTCTCAAGCTTCTTCTTGTCTTCCTTGAAGTGGGAGCAATCCTTGATGTGGGGGCAATCCGCAATGAAGTGCCCGGGCTCTTTGCACACATAGCA[T/C]
ACCCTTGCGGAGTGTCTTCCACTTGACTTGTTGGAGGAATGCTTGGACGAACTTCCCTTGAAGAAGCCGCTTTGCTTCATGAACTTGCCGAACTTCCCTT

Reverse complement sequence

AAGGGAAGTTCGGCAAGTTCATGAAGCAAAGCGGCTTCTTCAAGGGAAGTTCGTCCAAGCATTCCTCCAACAAGTCAAGTGGAAGACACTCCGCAAGGGT[A/G]
TGCTATGTGTGCAAAGAGCCCGGGCACTTCATTGCGGATTGCCCCCACATCAAGGATTGCTCCCACTTCAAGGAAGACAAGAAGAAGCTTGAGAAGAAGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.30%	24.70%	2.03%	7.02%	NA
All Indica	2759	94.30%	3.30%	2.14%	0.22%	NA
All Japonica	1512	11.00%	65.40%	2.12%	21.49%	NA
Aus	269	82.50%	17.10%	0.37%	0.00%	NA
Indica I	595	93.30%	2.20%	4.54%	0.00%	NA
Indica II	465	94.40%	4.50%	0.65%	0.43%	NA
Indica III	913	96.60%	2.50%	0.77%	0.11%	NA
Indica Intermediate	786	92.40%	4.50%	2.80%	0.38%	NA
Temperate Japonica	767	7.40%	69.60%	2.87%	20.08%	NA
Tropical Japonica	504	14.10%	54.20%	1.79%	29.96%	NA
Japonica Intermediate	241	15.80%	75.50%	0.41%	8.30%	NA
VI/Aromatic	96	92.70%	5.20%	2.08%	0.00%	NA
Intermediate	90	57.80%	38.90%	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
vg0711196263	T -> DEL	N	N	silent_mutation	Average:11.517; most accessible tissue: Callus, score: 30.512	N	N	N	N
vg0711196263	T -> C	LOC_Os07g18900.1	upstream_gene_variant ; 4064.0bp to feature; MODIFIER	silent_mutation	Average:11.517; most accessible tissue: Callus, score: 30.512	N	N	N	N
vg0711196263	T -> C	LOC_Os07g18890.1	intron_variant ; MODIFIER	silent_mutation	Average:11.517; most accessible tissue: Callus, score: 30.512	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711196263	1.53E-07	3.21E-07	mr1096	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
vg0711196263	NA	1.58E-11	mr1233	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
vg0711196263	9.67E-06	9.68E-06	mr1234	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
vg0711196263	2.94E-07	2.94E-07	mr1237	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
vg0711196263	1.51E-07	1.51E-07	mr1973	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