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Detailed information for vg1121358068:

Variant ID: vg1121358068 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21358068
Reference Allele: C	Alternative Allele: T,A
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:

ACGGTGGAGGTGGAGGAGGCGGAGGAGCCGGAGGAGATGGTGCAGGAGGAGGTGGCGGAGGAGCCAGAGGAGATGGTGCAGGAGGACGTGGCGGAGGAAC[C/T,A]
GGAGGATATGGTGCAGTAGGAGATGGCGGAGCCGGAGGAGATGGTGCACGAGACGCCGCTTGTCGCCCAGGGAGGATGATGTACCGCTTGCGCTATAGTA

Reverse complement sequence

TACTATAGCGCAAGCGGTACATCATCCTCCCTGGGCGACAAGCGGCGTCTCGTGCACCATCTCCTCCGGCTCCGCCATCTCCTACTGCACCATATCCTCC[G/A,T]
GTTCCTCCGCCACGTCCTCCTGCACCATCTCCTCTGGCTCCTCCGCCACCTCCTCCTGCACCATCTCCTCCGGCTCCTCCGCCTCCTCCACCTCCACCGT

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	90.20%	2.40%	4.42%	2.90%	A: 0.06%
All Indica	2759	85.70%	4.10%	6.09%	4.02%	A: 0.07%
All Japonica	1512	95.80%	0.10%	2.65%	1.52%	NA
Aus	269	99.30%	0.00%	0.37%	0.00%	A: 0.37%
Indica I	595	88.70%	1.20%	7.39%	2.69%	NA
Indica II	465	75.10%	12.30%	9.68%	3.01%	NA
Indica III	913	89.40%	1.40%	3.18%	5.81%	A: 0.22%
Indica Intermediate	786	85.50%	4.60%	6.36%	3.56%	NA
Temperate Japonica	767	93.90%	0.10%	4.17%	1.83%	NA
Tropical Japonica	504	97.80%	0.00%	0.79%	1.39%	NA
Japonica Intermediate	241	97.50%	0.00%	1.66%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	1.10%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121358068	C -> T	LOC_Os11g36280.1	intron_variant ; MODIFIER	silent_mutation	Average:38.398; most accessible tissue: Minghui63 young leaf, score: 75.937	N	N	N	N
vg1121358068	C -> A	LOC_Os11g36280.1	intron_variant ; MODIFIER	silent_mutation	Average:38.398; most accessible tissue: Minghui63 young leaf, score: 75.937	N	N	N	N
vg1121358068	C -> DEL	N	N	silent_mutation	Average:38.398; most accessible tissue: Minghui63 young leaf, score: 75.937	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121358068	NA	9.90E-06	mr1072	Ind_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
vg1121358068	NA	1.02E-06	mr1075	Ind_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
vg1121358068	NA	5.80E-06	mr1202	Ind_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
vg1121358068	NA	9.96E-07	mr1415	Ind_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
vg1121358068	NA	9.96E-07	mr1567	Ind_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
vg1121358068	9.28E-06	NA	mr1770	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
vg1121358068	4.59E-06	4.59E-06	mr1770	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
vg1121358068	NA	3.66E-06	mr1842	Ind_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