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Detailed information for vg1114474967:

Variant ID: vg1114474967 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14474967
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

CTATCTTCTTTAAATACTTTGGGCTATGTTCAGTTTGATGATTTTTGTGCGCTCGATAATTTGAAGGAGAAATTATTTGCTAAGTCTGATTTGCCATATC[C/A]
AACCAATGTTATATTTCACATTTTTGGCGAATATAATGATCTTGGAATATATTTTGTGCATAGAGTTTACATCTGCTCGGATTTAGAACTTACTGTACAT

Reverse complement sequence

ATGTACAGTAAGTTCTAAATCCGAGCAGATGTAAACTCTATGCACAAAATATATTCCAAGATCATTATATTCGCCAAAAATGTGAAATATAACATTGGTT[G/T]
GATATGGCAAATCAGACTTAGCAAATAATTTCTCCTTCAAATTATCGAGCGCACAAAAATCATCAAACTGAACATAGCCCAAAGTATTTAAAGAAGATAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.40%	16.40%	1.25%	0.00%	NA
All Indica	2759	70.90%	27.00%	2.10%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	77.10%	21.70%	1.18%	0.00%	NA
Indica II	465	48.80%	46.90%	4.30%	0.00%	NA
Indica III	913	78.00%	20.60%	1.42%	0.00%	NA
Indica Intermediate	786	71.10%	26.60%	2.29%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	26.70%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1114474967	C -> A	LOC_Os11g25400.1	downstream_gene_variant ; 4953.0bp to feature; MODIFIER	silent_mutation	Average:17.029; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg1114474967	C -> A	LOC_Os11g25390.1	intron_variant ; MODIFIER	silent_mutation	Average:17.029; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114474967	2.97E-06	2.97E-06	mr1349	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