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Detailed information for vg1112983207:

Variant ID: vg1112983207 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12983207
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCGGGGGCGGCTAGCCATCTAAACCGAAGAGGGCGAGGTAAGAATCAGATAAGCACTTAGGAGGGCAAGGAGCAAAGTAAATAACAACTCAGATAGCAC[G/A]
CACTAGGCATAAACTGGATTTTTCAAATCATAAAAACACCTGATACAACGGGTGTGGACAAGTCACAGAGCTACGCCGAGCTTGACTGTACGCACACCAC

Reverse complement sequence

GTGGTGTGCGTACAGTCAAGCTCGGCGTAGCTCTGTGACTTGTCCACACCCGTTGTATCAGGTGTTTTTATGATTTGAAAAATCCAGTTTATGCCTAGTG[C/T]
GTGCTATCTGAGTTGTTATTTACTTTGCTCCTTGCCCTCCTAAGTGCTTATCTGATTCTTACCTCGCCCTCTTCGGTTTAGATGGCTAGCCGCCCCCGCC

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	75.00%	0.30%	2.35%	22.39%	NA
All Indica	2759	59.30%	0.50%	3.73%	36.50%	NA
All Japonica	1512	98.70%	0.00%	0.40%	0.86%	NA
Aus	269	90.70%	0.00%	0.74%	8.55%	NA
Indica I	595	71.80%	0.30%	3.03%	24.87%	NA
Indica II	465	52.50%	0.20%	3.23%	44.09%	NA
Indica III	913	54.10%	0.70%	4.38%	40.85%	NA
Indica Intermediate	786	59.90%	0.50%	3.82%	35.75%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	97.40%	0.00%	1.19%	1.39%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	84.40%	0.00%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112983207	G -> A	LOC_Os11g22580.1	upstream_gene_variant ; 3389.0bp to feature; MODIFIER	silent_mutation	Average:8.992; most accessible tissue: Callus, score: 30.588	N	N	N	N
vg1112983207	G -> A	LOC_Os11g22570.1	intron_variant ; MODIFIER	silent_mutation	Average:8.992; most accessible tissue: Callus, score: 30.588	N	N	N	N
vg1112983207	G -> DEL	N	N	silent_mutation	Average:8.992; most accessible tissue: Callus, score: 30.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112983207	6.76E-07	NA	mr1241	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
vg1112983207	NA	2.57E-08	mr1595	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