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Detailed information for vg1105189380:

Variant ID: vg1105189380 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5189380
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.16, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGGGGCTCATCAGTCATCACAAGCAAATCTTTTGGCTTTGTACCCCGTCCGGCCGTCCCAGACTTAGCCTTCTTGGCCACCAACAAAATCCAACGCCG[T/C]
GAAGCCATCTCGTCCATGGAGCGGCGATGGCGAGCACGTTTGATGATGATATATGCCAACATGCCAACAATACGATGTGCGTCGTCGTGACTTGTTGTGA

Reverse complement sequence

TCACAACAAGTCACGACGACGCACATCGTATTGTTGGCATGTTGGCATATATCATCATCAAACGTGCTCGCCATCGCCGCTCCATGGACGAGATGGCTTC[A/G]
CGGCGTTGGATTTTGTTGGTGGCCAAGAAGGCTAAGTCTGGGACGGCCGGACGGGGTACAAAGCCAAAAGATTTGCTTGTGATGACTGATGAGCCCCTTC

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	57.40%	10.20%	0.89%	31.49%	NA
All Indica	2759	49.10%	0.80%	0.51%	49.58%	NA
All Japonica	1512	69.40%	29.30%	0.00%	1.26%	NA
Aus	269	65.40%	0.70%	9.29%	24.54%	NA
Indica I	595	24.20%	2.90%	0.34%	72.61%	NA
Indica II	465	20.00%	0.40%	1.29%	78.28%	NA
Indica III	913	72.90%	0.00%	0.22%	26.83%	NA
Indica Intermediate	786	57.50%	0.40%	0.51%	41.60%	NA
Temperate Japonica	767	64.00%	33.80%	0.00%	2.22%	NA
Tropical Japonica	504	85.90%	14.10%	0.00%	0.00%	NA
Japonica Intermediate	241	52.30%	46.90%	0.00%	0.83%	NA
VI/Aromatic	96	85.40%	4.20%	1.04%	9.38%	NA
Intermediate	90	54.40%	14.40%	2.22%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105189380	T -> DEL	N	N	silent_mutation	Average:13.045; most accessible tissue: Callus, score: 62.089	N	N	N	N
vg1105189380	T -> C	LOC_Os11g09720.1	downstream_gene_variant ; 1424.0bp to feature; MODIFIER	silent_mutation	Average:13.045; most accessible tissue: Callus, score: 62.089	N	N	N	N
vg1105189380	T -> C	LOC_Os11g09730.1	downstream_gene_variant ; 2990.0bp to feature; MODIFIER	silent_mutation	Average:13.045; most accessible tissue: Callus, score: 62.089	N	N	N	N
vg1105189380	T -> C	LOC_Os11g09720-LOC_Os11g09730	intergenic_region ; MODIFIER	silent_mutation	Average:13.045; most accessible tissue: Callus, score: 62.089	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105189380	4.09E-06	4.09E-06	mr1197	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
vg1105189380	6.83E-06	NA	mr1806_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251