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Detailed information for vg1112966318:

Variant ID: vg1112966318 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12966318
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCCACAGCGGTGTAACCCGTAGGTATACATAATCCCCTTCTTCGAAATTCAAATCCCTACAACGATTGTCTACATAGCTCTTCTGACGCGACTGGGCA[G/A]
TACGCAACCTTTCTTGGATAATCTTCACTTTTTCCTCTGCCTCTCGCAATATATCTGTCCCAAAAACTTGACGCTCACTGGTTTGATCCCAAAGGAGCGG

Reverse complement sequence

CCGCTCCTTTGGGATCAAACCAGTGAGCGTCAAGTTTTTGGGACAGATATATTGCGAGAGGCAGAGGAAAAAGTGAAGATTATCCAAGAAAGGTTGCGTA[C/T]
TGCCCAGTCGCGTCAGAAGAGCTATGTAGACAATCGTTGTAGGGATTTGAATTTCGAAGAAGGGGATTATGTATACCTACGGGTTACACCGCTGTGGGGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.30%	2.50%	24.44%	9.75%	NA
All Indica	2759	40.80%	4.20%	40.09%	14.93%	NA
All Japonica	1512	97.20%	0.10%	0.66%	2.12%	NA
Aus	269	88.80%	1.10%	9.29%	0.74%	NA
Indica I	595	63.70%	3.70%	30.08%	2.52%	NA
Indica II	465	38.30%	2.40%	41.29%	18.06%	NA
Indica III	913	25.30%	5.10%	42.28%	27.27%	NA
Indica Intermediate	786	42.90%	4.60%	44.40%	8.14%	NA
Temperate Japonica	767	99.30%	0.00%	0.13%	0.52%	NA
Tropical Japonica	504	93.50%	0.20%	1.79%	4.56%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	71.10%	0.00%	14.44%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112966318	G -> A	LOC_Os11g22560.1	downstream_gene_variant ; 4658.0bp to feature; MODIFIER	silent_mutation	Average:15.717; most accessible tissue: Callus, score: 46.831	N	N	N	N
vg1112966318	G -> A	LOC_Os11g22550.1	intron_variant ; MODIFIER	silent_mutation	Average:15.717; most accessible tissue: Callus, score: 46.831	N	N	N	N
vg1112966318	G -> DEL	N	N	silent_mutation	Average:15.717; most accessible tissue: Callus, score: 46.831	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112966318	5.80E-07	NA	mr1758_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