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Detailed information for vg1115128374:

Variant ID: vg1115128374 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15128374
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCTACTCCCTCAAAATCCATGTTCCAATTCCTGATGGCCCAGTATGCTCTACGCTCAAGCTCTACGGGGAGTCAGCATGACTTCCGGTAGACGATCTG[A/G]
TAGGGGGACATTCCAATGGGTGTCTTGTATGCTGTCTGGTATGCCCACAGTGCGTCTGGCAATTTCTCCTTCCATCCTGTTCCCATTTTGTTGACCGTCT

Reverse complement sequence

AGACGGTCAACAAAATGGGAACAGGATGGAAGGAGAAATTGCCAGACGCACTGTGGGCATACCAGACAGCATACAAGACACCCATTGGAATGTCCCCCTA[T/C]
CAGATCGTCTACCGGAAGTCATGCTGACTCCCCGTAGAGCTTGAGCGTAGAGCATACTGGGCCATCAGGAATTGGAACATGGATTTTGAGGGAGTAGGAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.10%	0.10%	16.02%	20.74%	NA
All Indica	2759	46.10%	0.10%	24.90%	28.85%	NA
All Japonica	1512	97.10%	0.00%	0.73%	2.18%	NA
Aus	269	31.60%	1.10%	17.84%	49.44%	NA
Indica I	595	39.70%	0.50%	30.42%	29.41%	NA
Indica II	465	47.10%	0.00%	26.24%	26.67%	NA
Indica III	913	48.80%	0.00%	19.61%	31.54%	NA
Indica Intermediate	786	47.20%	0.10%	26.08%	26.59%	NA
Temperate Japonica	767	96.90%	0.00%	1.04%	2.09%	NA
Tropical Japonica	504	97.80%	0.00%	0.40%	1.79%	NA
Japonica Intermediate	241	96.30%	0.00%	0.41%	3.32%	NA
VI/Aromatic	96	94.80%	0.00%	1.04%	4.17%	NA
Intermediate	90	73.30%	0.00%	11.11%	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
vg1115128374	A -> DEL	N	N	silent_mutation	Average:9.237; most accessible tissue: Callus, score: 29.071	N	N	N	N
vg1115128374	A -> G	LOC_Os11g26410.1	downstream_gene_variant ; 1194.0bp to feature; MODIFIER	silent_mutation	Average:9.237; most accessible tissue: Callus, score: 29.071	N	N	N	N
vg1115128374	A -> G	LOC_Os11g26400-LOC_Os11g26410	intergenic_region ; MODIFIER	silent_mutation	Average:9.237; most accessible tissue: Callus, score: 29.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115128374	3.60E-06	9.99E-06	mr1946	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