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Detailed information for vg1113029322:

Variant ID: vg1113029322 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13029322
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGTTCAAGTCCTAGAGAGAGCAACCGAAACCCGCACCACTCAAGAAGACTAAGTCTAACATGCAAGCAAAAGGTTATTCCAGTAGCAAGAGTCAGTAC[A/C]
TTAATGTACTGGCAAGCCAAAAATCAATCCTAACATACTACATGTAAGGCATATATTCAAAGGAGGGCAATATATAGTTTAATTTCAGCATAAAGCAAGT

Reverse complement sequence

ACTTGCTTTATGCTGAAATTAAACTATATATTGCCCTCCTTTGAATATATGCCTTACATGTAGTATGTTAGGATTGATTTTTGGCTTGCCAGTACATTAA[T/G]
GTACTGACTCTTGCTACTGGAATAACCTTTTGCTTGCATGTTAGACTTAGTCTTCTTGAGTGGTGCGGGTTTCGGTTGCTCTCTCTAGGACTTGAACTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.20%	2.30%	5.63%	1.88%	NA
All Indica	2759	87.80%	1.80%	7.61%	2.79%	NA
All Japonica	1512	99.90%	0.00%	0.00%	0.13%	NA
Aus	269	60.20%	21.60%	16.73%	1.49%	NA
Indica I	595	95.00%	0.70%	4.03%	0.34%	NA
Indica II	465	82.20%	2.40%	11.61%	3.87%	NA
Indica III	913	89.20%	1.30%	6.02%	3.50%	NA
Indica Intermediate	786	84.20%	2.80%	9.80%	3.18%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	1.00%	5.21%	1.04%	NA
Intermediate	90	86.70%	1.10%	6.67%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1113029322	A -> DEL	N	N	silent_mutation	Average:22.649; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg1113029322	A -> C	LOC_Os11g22650.1	upstream_gene_variant ; 2943.0bp to feature; MODIFIER	silent_mutation	Average:22.649; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg1113029322	A -> C	LOC_Os11g22640-LOC_Os11g22650	intergenic_region ; MODIFIER	silent_mutation	Average:22.649; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113029322	NA	5.51E-07	mr1360_2	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
vg1113029322	NA	8.89E-06	mr1748_2	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
vg1113029322	1.72E-06	6.75E-07	mr1893_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