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Detailed information for vg0911767318:

Variant ID: vg0911767318 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11767318
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCCGTCCACCCACCCGGCCACATTATTTCGGGACAAATTCGGGTCAAAAATTCGGGTACCTAGGACTTTTTACGGATATTGGGTCCGAATACGGGTCT[T/C]
TTGTGGATACGAGATCGGGTTCGGGAACATAATATCTGACGGATACGGATTATCCGGCAAAAAATCCGGGTATTACCCGGATAAATATTCGGATATTACC

Reverse complement sequence

GGTAATATCCGAATATTTATCCGGGTAATACCCGGATTTTTTGCCGGATAATCCGTATCCGTCAGATATTATGTTCCCGAACCCGATCTCGTATCCACAA[A/G]
AGACCCGTATTCGGACCCAATATCCGTAAAAAGTCCTAGGTACCCGAATTTTTGACCCGAATTTGTCCCGAAATAATGTGGCCGGGTGGGTGGACGGAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.10%	8.40%	0.06%	1.40%	NA
All Indica	2759	83.30%	14.40%	0.07%	2.25%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.00%	NA
Aus	269	98.90%	0.00%	0.00%	1.12%	NA
Indica I	595	83.00%	17.00%	0.00%	0.00%	NA
Indica II	465	89.20%	8.00%	0.00%	2.80%	NA
Indica III	913	81.70%	13.50%	0.00%	4.82%	NA
Indica Intermediate	786	81.90%	17.20%	0.25%	0.64%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911767318	T -> DEL	N	N	silent_mutation	Average:58.209; most accessible tissue: Callus, score: 80.925	N	N	N	N
vg0911767318	T -> C	LOC_Os09g19670.1	upstream_gene_variant ; 410.0bp to feature; MODIFIER	silent_mutation	Average:58.209; most accessible tissue: Callus, score: 80.925	N	N	N	N
vg0911767318	T -> C	LOC_Os09g19650-LOC_Os09g19670	intergenic_region ; MODIFIER	silent_mutation	Average:58.209; most accessible tissue: Callus, score: 80.925	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911767318	NA	3.31E-06	mr1125	Ind_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
vg0911767318	NA	2.73E-06	mr1163	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