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Detailed information for vg1118796541:

Variant ID: vg1118796541 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18796541
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

ACCATTCGACGCGTACGTCGTGCACGCGCGCCGCCTGCCCTGCCAGGCCAGGCGAGGCGAGGCGAGTGAGTGCGCGCGTGTGTTCCCCCTCTTCTCTCCA[C/T]
CACACATGCTTCAAGTGGCTAGGAGGGCATCCTCCCTTTTAAGGAGGTCCCTCTTTCCTAGAATAAACAAGGTGGTACTAAACTCCACATGCATGCCATC

Reverse complement sequence

GATGGCATGCATGTGGAGTTTAGTACCACCTTGTTTATTCTAGGAAAGAGGGACCTCCTTAAAAGGGAGGATGCCCTCCTAGCCACTTGAAGCATGTGTG[G/A]
TGGAGAGAAGAGGGGGAACACACGCGCGCACTCACTCGCCTCGCCTCGCCTGGCCTGGCAGGGCAGGCGGCGCGCGTGCACGACGTACGCGTCGAATGGT

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	80.90%	18.20%	0.85%	0.00%	NA
All Indica	2759	68.10%	30.50%	1.38%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.07%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	48.40%	50.30%	1.34%	0.00%	NA
Indica II	465	56.60%	42.20%	1.29%	0.00%	NA
Indica III	913	79.50%	19.20%	1.31%	0.00%	NA
Indica Intermediate	786	76.60%	21.90%	1.53%	0.00%	NA
Temperate Japonica	767	99.30%	0.50%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg1118796541	C -> T	LOC_Os11g31970.1	downstream_gene_variant ; 815.0bp to feature; MODIFIER	silent_mutation	Average:33.156; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N
vg1118796541	C -> T	LOC_Os11g31950-LOC_Os11g31970	intergenic_region ; MODIFIER	silent_mutation	Average:33.156; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118796541	NA	5.50E-06	mr1312	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
vg1118796541	NA	7.59E-08	mr1377	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
vg1118796541	4.16E-06	NA	mr1721	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