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Detailed information for vg1123141598:

Variant ID: vg1123141598 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23141598
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTATTACAAATATTGTGAATAATTGCTCTTGTGCTAAGAAAATAAATTTATATCCTTGTCACCTAAATTTCCTTTTAGCCTCAAACAATTCCTTGAAACC[C/T]
ATGCCATATATTTTAGGGTTCAAATCCTATCCTTTTGCCTCCACATATTTTCCTACCACATTCCAAAAAATATTTTGAGGAATACTATTAATTTACTTTT

Reverse complement sequence

AAAAGTAAATTAATAGTATTCCTCAAAATATTTTTTGGAATGTGGTAGGAAAATATGTGGAGGCAAAAGGATAGGATTTGAACCCTAAAATATATGGCAT[G/A]
GGTTTCAAGGAATTGTTTGAGGCTAAAAGGAAATTTAGGTGACAAGGATATAAATTTATTTTCTTAGCACAAGAGCAATTATTCACAATATTTGTAATAA

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	83.40%	14.90%	1.69%	0.00%	NA
All Indica	2759	82.60%	16.90%	0.51%	0.00%	NA
All Japonica	1512	97.80%	1.50%	0.66%	0.00%	NA
Aus	269	36.80%	46.50%	16.73%	0.00%	NA
Indica I	595	95.10%	4.50%	0.34%	0.00%	NA
Indica II	465	90.80%	9.00%	0.22%	0.00%	NA
Indica III	913	69.80%	29.10%	1.10%	0.00%	NA
Indica Intermediate	786	83.30%	16.50%	0.13%	0.00%	NA
Temperate Japonica	767	97.40%	1.70%	0.91%	0.00%	NA
Tropical Japonica	504	98.60%	1.20%	0.20%	0.00%	NA
Japonica Intermediate	241	97.50%	1.70%	0.83%	0.00%	NA
VI/Aromatic	96	18.80%	75.00%	6.25%	0.00%	NA
Intermediate	90	72.20%	22.20%	5.56%	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
vg1123141598	C -> T	LOC_Os11g38870.1	upstream_gene_variant ; 4000.0bp to feature; MODIFIER	silent_mutation	Average:47.83; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N
vg1123141598	C -> T	LOC_Os11g38870.2	upstream_gene_variant ; 4000.0bp to feature; MODIFIER	silent_mutation	Average:47.83; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N
vg1123141598	C -> T	LOC_Os11g38880.1	intron_variant ; MODIFIER	silent_mutation	Average:47.83; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123141598	3.13E-06	3.13E-06	mr1744_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
vg1123141598	NA	1.27E-06	mr1994_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