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Detailed information for vg1106417917:

Variant ID: vg1106417917 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6417917
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

GCGTGCCCGCCGGCATCGACCGGAGCAAGATCCACGCCGCCGGCAGCGACGGGCTCTGCCTCGTCAACGACGGCCTGCAGATCGTGAAGGGGTCGCCGGT[G/T]
GTGTTCACGTACGCCGCCAGCGCGCCCATCAGCCTCGCCTTCAACGCCGCCTCGCCGCGGTGCCAACCTTGAGTTTGGCTGTAGGCCTACCATTGTTTGC

Reverse complement sequence

GCAAACAATGGTAGGCCTACAGCCAAACTCAAGGTTGGCACCGCGGCGAGGCGGCGTTGAAGGCGAGGCTGATGGGCGCGCTGGCGGCGTACGTGAACAC[C/A]
ACCGGCGACCCCTTCACGATCTGCAGGCCGTCGTTGACGAGGCAGAGCCCGTCGCTGCCGGCGGCGTGGATCTTGCTCCGGTCGATGCCGGCGGGCACGC

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	46.50%	18.60%	10.01%	24.90%	NA
All Indica	2759	23.20%	28.80%	15.98%	32.04%	NA
All Japonica	1512	91.00%	4.20%	0.93%	3.90%	NA
Aus	269	16.40%	0.70%	3.35%	79.55%	NA
Indica I	595	23.00%	31.10%	23.53%	22.35%	NA
Indica II	465	9.90%	34.20%	24.73%	31.18%	NA
Indica III	913	29.60%	24.50%	6.68%	39.21%	NA
Indica Intermediate	786	23.70%	28.90%	15.90%	31.55%	NA
Temperate Japonica	767	93.10%	2.30%	0.91%	3.65%	NA
Tropical Japonica	504	90.30%	5.80%	0.99%	2.98%	NA
Japonica Intermediate	241	85.90%	6.60%	0.83%	6.64%	NA
VI/Aromatic	96	93.80%	0.00%	1.04%	5.21%	NA
Intermediate	90	53.30%	21.10%	8.89%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106417917	G -> T	LOC_Os11g11540.1	synonymous_variant ; p.Val115Val; LOW	synonymous_codon	Average:14.25; most accessible tissue: Callus, score: 43.853	N	N	N	N
vg1106417917	G -> DEL	LOC_Os11g11540.1	N	frameshift_variant	Average:14.25; most accessible tissue: Callus, score: 43.853	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106417917	9.38E-07	NA	mr1255	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