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Detailed information for vg0111460968:

Variant ID: vg0111460968 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 11460968
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTTTGACTTCTTCTTTCTATAAAAATATTCATTGAAAAGTGATATATGTATACTTTTATGAAAGTATTTTTCAAGACAAATTTATTCATATAATTTTTA[C/T]
ATTTTCAAACTCAACAACTTGAGAGTTATTTATGATTTATAATCTCAAGGTTTGACTTAAACATTGTCTTAAACGACTTCCTTTATGAGTATGAAGGGAG

Reverse complement sequence

CTCCCTTCATACTCATAAAGGAAGTCGTTTAAGACAATGTTTAAGTCAAACCTTGAGATTATAAATCATAAATAACTCTCAAGTTGTTGAGTTTGAAAAT[G/A]
TAAAAATTATATGAATAAATTTGTCTTGAAAAATACTTTCATAAAAGTATACATATATCACTTTTCAATGAATATTTTTATAGAAAGAAGAAGTCAAAGT

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	93.60%	6.40%	0.02%	0.00%	NA
All Indica	2759	89.10%	10.90%	0.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	97.40%	2.60%	0.00%	0.00%	NA
Indica III	913	76.00%	24.00%	0.00%	0.00%	NA
Indica Intermediate	786	91.90%	8.00%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	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	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0111460968	C -> T	LOC_Os01g20160.1	intron_variant ; MODIFIER	silent_mutation	Average:52.663; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0111460968	1.96E-06	2.35E-06	mr1117	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
vg0111460968	NA	5.38E-06	mr1121	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
vg0111460968	NA	2.25E-06	mr1533_2	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