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Detailed information for vg1121543479:

Variant ID: vg1121543479 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21543479
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCGCACACAACAGGTAAATATGAACCAAGAACCGCAGATGCACAGCAACATTCAATCCTATATGCAGCGTATAATATATCAACGGTGTGCAGATACCAG[A/C]
AGCTACGGTAGTTTACTCTGCAAAACGATTGTAAGTATCCCCTCCGGTTTTTTAGATGGCGTCTTTGACTTTTGAACATTTTTCTTACTAAAAAATTACA

Reverse complement sequence

TGTAATTTTTTAGTAAGAAAAATGTTCAAAAGTCAAAGACGCCATCTAAAAAACCGGAGGGGATACTTACAATCGTTTTGCAGAGTAAACTACCGTAGCT[T/G]
CTGGTATCTGCACACCGTTGATATATTATACGCTGCATATAGGATTGAATGTTGCTGTGCATCTGCGGTTCTTGGTTCATATTTACCTGTTGTGTGCGGG

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	60.20%	0.60%	3.11%	36.12%	NA
All Indica	2759	50.70%	0.80%	2.94%	45.49%	NA
All Japonica	1512	77.60%	0.20%	1.85%	20.30%	NA
Aus	269	79.90%	0.00%	6.32%	13.75%	NA
Indica I	595	66.20%	0.70%	2.02%	31.09%	NA
Indica II	465	44.90%	2.40%	2.58%	50.11%	NA
Indica III	913	45.20%	0.30%	3.29%	51.15%	NA
Indica Intermediate	786	48.90%	0.60%	3.44%	47.07%	NA
Temperate Japonica	767	89.40%	0.10%	1.04%	9.39%	NA
Tropical Japonica	504	62.70%	0.40%	3.37%	33.53%	NA
Japonica Intermediate	241	71.40%	0.00%	1.24%	27.39%	NA
VI/Aromatic	96	5.20%	1.00%	16.67%	77.08%	NA
Intermediate	90	55.60%	1.10%	5.56%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121543479	A -> DEL	N	N	silent_mutation	Average:31.2; most accessible tissue: Callus, score: 80.18	N	N	N	N
vg1121543479	A -> C	LOC_Os11g36500.1	upstream_gene_variant ; 3990.0bp to feature; MODIFIER	silent_mutation	Average:31.2; most accessible tissue: Callus, score: 80.18	N	N	N	N
vg1121543479	A -> C	LOC_Os11g36510.1	intron_variant ; MODIFIER	silent_mutation	Average:31.2; most accessible tissue: Callus, score: 80.18	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121543479	3.97E-06	NA	mr1233	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