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Detailed information for vg1121372738:

Variant ID: vg1121372738 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21372738
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: 272. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGAAAAGGCGATCCTAGCGGGGCTTCAACTCCACTCCACAGGCAAAACTCAACTGGGGTCTGAGCCTTAGTCTTCTAACTTCGTCTTCAGCTCAGAAG[C/T]
GCTATTACTTCTAAAAAGGGGAACAATAGCAAGGCTGAGTATAACAACCGTACTCATCAAGCCATACTAACGATGCAGACGTGCAAGGGGATACAAGGAT

Reverse complement sequence

ATCCTTGTATCCCCTTGCACGTCTGCATCGTTAGTATGGCTTGATGAGTACGGTTGTTATACTCAGCCTTGCTATTGTTCCCCTTTTTAGAAGTAATAGC[G/A]
CTTCTGAGCTGAAGACGAAGTTAGAAGACTAAGGCTCAGACCCCAGTTGAGTTTTGCCTGTGGAGTGGAGTTGAAGCCCCGCTAGGATCGCCTTTTCTGC

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	22.20%	3.70%	5.61%	68.41%	NA
All Indica	2759	7.00%	0.40%	5.04%	87.53%	NA
All Japonica	1512	48.20%	10.80%	6.48%	34.52%	NA
Aus	269	20.10%	0.00%	1.86%	78.07%	NA
Indica I	595	20.80%	0.20%	3.03%	75.97%	NA
Indica II	465	2.60%	0.20%	5.59%	91.61%	NA
Indica III	913	1.30%	1.00%	4.82%	92.88%	NA
Indica Intermediate	786	5.90%	0.00%	6.49%	87.66%	NA
Temperate Japonica	767	68.10%	4.80%	6.78%	20.34%	NA
Tropical Japonica	504	26.60%	16.10%	5.16%	52.18%	NA
Japonica Intermediate	241	30.30%	18.70%	8.30%	42.74%	NA
VI/Aromatic	96	45.80%	0.00%	17.71%	36.46%	NA
Intermediate	90	33.30%	3.30%	6.67%	56.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121372738	C -> T	LOC_Os11g36280.1	upstream_gene_variant ; 4219.0bp to feature; MODIFIER	silent_mutation	Average:42.504; most accessible tissue: Zhenshan97 root, score: 53.045	N	N	N	N
vg1121372738	C -> T	LOC_Os11g36300.1	upstream_gene_variant ; 2136.0bp to feature; MODIFIER	silent_mutation	Average:42.504; most accessible tissue: Zhenshan97 root, score: 53.045	N	N	N	N
vg1121372738	C -> T	LOC_Os11g36290.1	downstream_gene_variant ; 287.0bp to feature; MODIFIER	silent_mutation	Average:42.504; most accessible tissue: Zhenshan97 root, score: 53.045	N	N	N	N
vg1121372738	C -> T	LOC_Os11g36290-LOC_Os11g36300	intergenic_region ; MODIFIER	silent_mutation	Average:42.504; most accessible tissue: Zhenshan97 root, score: 53.045	N	N	N	N
vg1121372738	C -> DEL	N	N	silent_mutation	Average:42.504; most accessible tissue: Zhenshan97 root, score: 53.045	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121372738	6.53E-09	6.53E-09	mr1766	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
vg1121372738	3.36E-06	2.31E-06	mr1871	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