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Detailed information for vg1107383686:

Variant ID: vg1107383686 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7383686
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.02, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCGAGATGAGGGGCACTGGAAAGGGATGTATCGCGACTTCAGGCCATCCCGAAGTCGGAAACCGACACATCCGGACACCTTTTTAGGTTCCATCCAGC[T/G]
CAACTCATAATAAAAGTGGAAGAGGTCAAGAAACGGCTCTACCCCAATGTAGGCCTCACAAAGATGCGAAAAGATACTGAGGAAGGCGATGGAATTGGGG

Reverse complement sequence

CCCCAATTCCATCGCCTTCCTCAGTATCTTTTCGCATCTTTGTGAGGCCTACATTGGGGTAGAGCCGTTTCTTGACCTCTTCCACTTTTATTATGAGTTG[A/C]
GCTGGATGGAACCTAAAAAGGTGTCCGGATGTGTCGGTTTCCGACTTCGGGATGGCCTGAAGTCGCGATACATCCCTTTCCAGTGCCCCTCATCTCGCAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.70%	22.70%	0.91%	33.73%	NA
All Indica	2759	47.20%	2.30%	1.30%	49.18%	NA
All Japonica	1512	32.80%	59.40%	0.33%	7.47%	NA
Aus	269	63.90%	0.40%	0.74%	34.94%	NA
Indica I	595	23.20%	1.70%	1.18%	73.95%	NA
Indica II	465	68.40%	0.60%	0.43%	30.54%	NA
Indica III	913	55.30%	1.30%	1.97%	41.40%	NA
Indica Intermediate	786	43.40%	5.00%	1.15%	50.51%	NA
Temperate Japonica	767	33.50%	63.10%	0.39%	3.00%	NA
Tropical Japonica	504	37.10%	53.40%	0.40%	9.13%	NA
Japonica Intermediate	241	21.60%	60.20%	0.00%	18.26%	NA
VI/Aromatic	96	14.60%	83.30%	0.00%	2.08%	NA
Intermediate	90	36.70%	32.20%	0.00%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107383686	T -> DEL	N	N	silent_mutation	Average:23.596; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1107383686	T -> G	LOC_Os11g13459.1	downstream_gene_variant ; 3681.0bp to feature; MODIFIER	silent_mutation	Average:23.596; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1107383686	T -> G	LOC_Os11g13480.1	intron_variant ; MODIFIER	silent_mutation	Average:23.596; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107383686	2.15E-06	3.14E-08	mr1260_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