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Detailed information for vg1106677250:

Variant ID: vg1106677250 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6677250
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.80, G: 0.22, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

ATCACCATTCTACATACTATTTAAATTTAAATTATCATAAACCACATTAATTTACTTAATCTGATATTATCTAGCTATCTTACACGTTATTTTTTTTATT[T/G]
TTATCATACTAAATTCCCGCAGCAATGCGCGGGGTTTCAGCTAGTATTTTCTACTTATAGACCTGTAGGAAAAAAACATTAAAGAAATGGACCCTTTTGA

Reverse complement sequence

TCAAAAGGGTCCATTTCTTTAATGTTTTTTTCCTACAGGTCTATAAGTAGAAAATACTAGCTGAAACCCCGCGCATTGCTGCGGGAATTTAGTATGATAA[A/C]
AATAAAAAAAATAACGTGTAAGATAGCTAGATAATATCAGATTAAGTAAATTAATGTGGTTTATGATAATTTAAATTTAAATAGTATGTAGAATGGTGAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.50%	18.50%	0.80%	54.17%	NA
All Indica	2759	3.20%	29.70%	1.12%	65.93%	NA
All Japonica	1512	58.70%	1.30%	0.20%	39.81%	NA
Aus	269	85.50%	5.90%	0.37%	8.18%	NA
Indica I	595	1.30%	14.10%	1.01%	83.53%	NA
Indica II	465	1.50%	22.40%	1.08%	75.05%	NA
Indica III	913	3.70%	43.60%	1.31%	51.37%	NA
Indica Intermediate	786	5.10%	29.80%	1.02%	64.12%	NA
Temperate Japonica	767	93.20%	0.70%	0.00%	6.13%	NA
Tropical Japonica	504	7.10%	2.00%	0.60%	90.28%	NA
Japonica Intermediate	241	56.80%	1.70%	0.00%	41.49%	NA
VI/Aromatic	96	27.10%	2.10%	1.04%	69.79%	NA
Intermediate	90	22.20%	20.00%	2.22%	55.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106677250	T -> DEL	N	N	silent_mutation	Average:14.056; most accessible tissue: Callus, score: 72.866	N	N	N	N
vg1106677250	T -> G	LOC_Os11g12000.1	intron_variant ; MODIFIER	silent_mutation	Average:14.056; most accessible tissue: Callus, score: 72.866	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106677250	2.22E-07	2.22E-07	mr1973_2	Jap_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