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Detailed information for vg1128859381:

Variant ID: vg1128859381 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28859381
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCCAGGTGTCGGGTTTTCCAAGTCTTTTGTAAAACCCAAGTTTTACCCAAGATGTTTTTTAGATTTTAAGTTTGAAGGCGACCGTCGATACTCGTGTAG[A/G]
GTGCACGATTTCCGAGGCGCAACTGGGTGGTTACAAGGAAACATGGTATAACAATTAACAGAGGAAGGATCAAATGCAACAAGCTAGGTAGGTCCGCCAA

Reverse complement sequence

TTGGCGGACCTACCTAGCTTGTTGCATTTGATCCTTCCTCTGTTAATTGTTATACCATGTTTCCTTGTAACCACCCAGTTGCGCCTCGGAAATCGTGCAC[T/C]
CTACACGAGTATCGACGGTCGCCTTCAAACTTAAAATCTAAAAAACATCTTGGGTAAAACTTGGGTTTTACAAAAGACTTGGAAAACCCGACACCTGGGT

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	87.90%	3.10%	4.13%	4.89%	NA
All Indica	2759	86.90%	5.20%	5.51%	2.36%	NA
All Japonica	1512	88.80%	0.00%	0.99%	10.25%	NA
Aus	269	92.20%	0.40%	5.95%	1.49%	NA
Indica I	595	95.00%	1.00%	1.85%	2.18%	NA
Indica II	465	85.80%	3.40%	2.80%	7.96%	NA
Indica III	913	78.40%	10.40%	11.06%	0.11%	NA
Indica Intermediate	786	91.30%	3.40%	3.44%	1.78%	NA
Temperate Japonica	767	88.40%	0.00%	0.91%	10.69%	NA
Tropical Japonica	504	88.50%	0.00%	0.79%	10.71%	NA
Japonica Intermediate	241	90.50%	0.00%	1.66%	7.88%	NA
VI/Aromatic	96	86.50%	0.00%	8.33%	5.21%	NA
Intermediate	90	91.10%	2.20%	4.44%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128859381	A -> DEL	N	N	silent_mutation	Average:11.455; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1128859381	A -> G	LOC_Os11g47840.1	upstream_gene_variant ; 1860.0bp to feature; MODIFIER	silent_mutation	Average:11.455; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1128859381	A -> G	LOC_Os11g47850.1	upstream_gene_variant ; 1437.0bp to feature; MODIFIER	silent_mutation	Average:11.455; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg1128859381	A -> G	LOC_Os11g47840-LOC_Os11g47850	intergenic_region ; MODIFIER	silent_mutation	Average:11.455; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128859381	3.93E-06	3.93E-06	mr1250_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