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Detailed information for vg0113992286:

Variant ID: vg0113992286 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13992286
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: 0.17, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

GTTATTGATCAGTTTCGACCGTCAATATTACCAAAATAGAGGAGAACTAGTGATGCTTGCAATGCATATACATGTTAGAATAATAATATTCCACTAGGTT[T/C]
ACTAACCTTTTGTAGAGAATAACCATAAAGTGGAGGAGAATCGACATCAACTCAAACGATAAATTAATCGGACGATGTCGAGAATCAGACTTATGCATGA

Reverse complement sequence

TCATGCATAAGTCTGATTCTCGACATCGTCCGATTAATTTATCGTTTGAGTTGATGTCGATTCTCCTCCACTTTATGGTTATTCTCTACAAAAGGTTAGT[A/G]
AACCTAGTGGAATATTATTATTCTAACATGTATATGCATTGCAAGCATCACTAGTTCTCCTCTATTTTGGTAATATTGACGGTCGAAACTGATCAATAAC

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	43.20%	36.30%	13.22%	7.26%	NA
All Indica	2759	61.30%	6.20%	20.37%	12.14%	NA
All Japonica	1512	4.40%	95.50%	0.07%	0.00%	NA
Aus	269	79.60%	3.00%	15.99%	1.49%	NA
Indica I	595	66.40%	4.50%	28.24%	0.84%	NA
Indica II	465	61.10%	8.20%	19.78%	10.97%	NA
Indica III	913	54.70%	4.70%	16.76%	23.88%	NA
Indica Intermediate	786	65.40%	7.90%	18.96%	7.76%	NA
Temperate Japonica	767	1.80%	98.20%	0.00%	0.00%	NA
Tropical Japonica	504	9.50%	90.30%	0.20%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	41.70%	51.00%	6.25%	1.04%	NA
Intermediate	90	31.10%	51.10%	14.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113992286	T -> DEL	N	N	silent_mutation	Average:27.304; most accessible tissue: Callus, score: 51.369	N	N	N	N
vg0113992286	T -> C	LOC_Os01g24840.1	upstream_gene_variant ; 3575.0bp to feature; MODIFIER	silent_mutation	Average:27.304; most accessible tissue: Callus, score: 51.369	N	N	N	N
vg0113992286	T -> C	LOC_Os01g24840-LOC_Os01g24860	intergenic_region ; MODIFIER	silent_mutation	Average:27.304; most accessible tissue: Callus, score: 51.369	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113992286	NA	6.47E-20	mr1102	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
vg0113992286	NA	6.38E-45	mr1141	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
vg0113992286	NA	2.84E-60	mr1141_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
vg0113992286	NA	3.92E-15	mr1277_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
vg0113992286	NA	4.26E-24	mr1403_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
vg0113992286	NA	3.01E-19	mr1416_2	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
vg0113992286	NA	8.27E-44	mr1519_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
vg0113992286	NA	7.08E-19	mr1637_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
vg0113992286	NA	1.46E-09	mr1705_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
vg0113992286	NA	2.15E-32	mr1780_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