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Detailed information for vg1116351931:

Variant ID: vg1116351931 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16351931
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCGTCCGCCGCCGCTGTGAGAGTGTGACATCTCTTTGTAGGTTTGTCCTGAAAACCTTCCGTTTTGCCCACGAGACGGGTAGCTATCTAGAAATCGGCT[C/T]
CGCTAGCCGGTTTAGTTATCAAAACCCATCTAGGTTTAGGTCTTTGCTAGATTGAGGTGGTTGGCGACTCTAGGATCACCGCAAGGCTTAAGGTGCTACG

Reverse complement sequence

CGTAGCACCTTAAGCCTTGCGGTGATCCTAGAGTCGCCAACCACCTCAATCTAGCAAAGACCTAAACCTAGATGGGTTTTGATAACTAAACCGGCTAGCG[G/A]
AGCCGATTTCTAGATAGCTACCCGTCTCGTGGGCAAAACGGAAGGTTTTCAGGACAAACCTACAAAGAGATGTCACACTCTCACAGCGGCGGCGGACGGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.60%	3.50%	4.74%	47.16%	NA
All Indica	2759	33.50%	5.00%	5.51%	56.03%	NA
All Japonica	1512	57.30%	1.90%	3.24%	37.57%	NA
Aus	269	66.90%	0.00%	7.43%	25.65%	NA
Indica I	595	17.00%	7.60%	3.53%	71.93%	NA
Indica II	465	30.80%	2.60%	5.16%	61.51%	NA
Indica III	913	46.70%	5.10%	5.15%	43.04%	NA
Indica Intermediate	786	32.30%	4.20%	7.63%	55.85%	NA
Temperate Japonica	767	84.60%	1.00%	0.52%	13.82%	NA
Tropical Japonica	504	29.20%	3.00%	7.14%	60.71%	NA
Japonica Intermediate	241	29.50%	2.10%	3.73%	64.73%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	46.70%	0.00%	3.33%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116351931	C -> T	LOC_Os11g28400.1	downstream_gene_variant ; 2999.0bp to feature; MODIFIER	silent_mutation	Average:20.191; most accessible tissue: Callus, score: 66.567	N	N	N	N
vg1116351931	C -> T	LOC_Os11g28410.1	intron_variant ; MODIFIER	silent_mutation	Average:20.191; most accessible tissue: Callus, score: 66.567	N	N	N	N
vg1116351931	C -> DEL	N	N	silent_mutation	Average:20.191; most accessible tissue: Callus, score: 66.567	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116351931	3.90E-06	NA	mr1503	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