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Detailed information for vg1124416534:

Variant ID: vg1124416534 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24416534
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, C: 0.16, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTAAAGGAGTTATTATATTATAAAAGTATTATTCAACACGGCACTATCACAGAACAGCTTATCAGTGCCGGTTCAAGATAACTCGATACTGATGATGG[T/C]
TTTCCGTCCCAAAATACAAGCTTGCGCCATGCATATGTTCTCTTGGCACTGATGGGGAGATATCAGTACCGGGTCTTACAACCATTCGGCACTAATTGTT

Reverse complement sequence

AACAATTAGTGCCGAATGGTTGTAAGACCCGGTACTGATATCTCCCCATCAGTGCCAAGAGAACATATGCATGGCGCAAGCTTGTATTTTGGGACGGAAA[A/G]
CCATCATCAGTATCGAGTTATCTTGAACCGGCACTGATAAGCTGTTCTGTGATAGTGCCGTGTTGAATAATACTTTTATAATATAATAACTCCTTTAGGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.30%	34.40%	0.28%	0.00%	NA
All Indica	2759	59.80%	39.80%	0.40%	0.00%	NA
All Japonica	1512	81.00%	19.00%	0.07%	0.00%	NA
Aus	269	50.60%	49.40%	0.00%	0.00%	NA
Indica I	595	74.50%	25.20%	0.34%	0.00%	NA
Indica II	465	54.00%	45.60%	0.43%	0.00%	NA
Indica III	913	56.80%	43.00%	0.11%	0.00%	NA
Indica Intermediate	786	55.70%	43.50%	0.76%	0.00%	NA
Temperate Japonica	767	80.40%	19.60%	0.00%	0.00%	NA
Tropical Japonica	504	80.60%	19.20%	0.20%	0.00%	NA
Japonica Intermediate	241	83.40%	16.60%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	71.10%	27.80%	1.11%	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
vg1124416534	T -> C	LOC_Os11g40800.1	downstream_gene_variant ; 737.0bp to feature; MODIFIER	silent_mutation	Average:56.87; most accessible tissue: Callus, score: 80.009	N	N	N	N
vg1124416534	T -> C	LOC_Os11g40800-LOC_Os11g40810	intergenic_region ; MODIFIER	silent_mutation	Average:56.87; most accessible tissue: Callus, score: 80.009	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124416534	NA	3.75E-06	mr1309	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
vg1124416534	3.12E-06	NA	mr1771	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
vg1124416534	NA	9.51E-06	mr1238_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
vg1124416534	NA	4.50E-08	mr1609_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
vg1124416534	NA	5.59E-06	mr1768_2	Jap_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
vg1124416534	NA	7.96E-06	mr1900_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