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Detailed information for vg0414013336:

Variant ID: vg0414013336 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14013336
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

GTAGAGAGCATCTTCCGACCAAGACAACACCGAAACCAGCCCACATCGCAGCTCAATTTATTCCATTGATACCGATGTATGAAATACTAACTACTACTTG[C/T]
GTGAGATTTGTGTACAATGTGTAATCATATATATGGTGTGTTTATTATTGATTGGCAATATGTACATACGATTGTTTATTGATTTACAATGCAACATCCT

Reverse complement sequence

AGGATGTTGCATTGTAAATCAATAAACAATCGTATGTACATATTGCCAATCAATAATAAACACACCATATATATGATTACACATTGTACACAAATCTCAC[G/A]
CAAGTAGTAGTTAGTATTTCATACATCGGTATCAATGGAATAAATTGAGCTGCGATGTGGGCTGGTTTCGGTGTTGTCTTGGTCGGAAGATGCTCTCTAC

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	42.40%	23.80%	21.77%	11.98%	NA
All Indica	2759	52.80%	40.40%	5.29%	1.52%	NA
All Japonica	1512	12.90%	0.20%	53.31%	33.60%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	24.50%	55.60%	15.13%	4.71%	NA
Indica II	465	74.80%	23.00%	1.51%	0.65%	NA
Indica III	913	58.70%	40.30%	0.88%	0.11%	NA
Indica Intermediate	786	54.30%	39.20%	5.22%	1.27%	NA
Temperate Japonica	767	6.80%	0.30%	42.37%	50.59%	NA
Tropical Japonica	504	23.40%	0.20%	73.81%	2.58%	NA
Japonica Intermediate	241	10.40%	0.00%	45.23%	44.40%	NA
VI/Aromatic	96	45.80%	0.00%	45.83%	8.33%	NA
Intermediate	90	47.80%	10.00%	33.33%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414013336	C -> DEL	N	N	silent_mutation	Average:13.181; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0414013336	C -> T	LOC_Os04g24430.1	3_prime_UTR_variant ; 97.0bp to feature; MODIFIER	silent_mutation	Average:13.181; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0414013336	C -> T	LOC_Os04g24440.1	downstream_gene_variant ; 1729.0bp to feature; MODIFIER	silent_mutation	Average:13.181; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414013336	NA	8.92E-06	mr1386	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
vg0414013336	NA	4.92E-08	mr1830	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
vg0414013336	NA	4.25E-10	mr1846	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
vg0414013336	NA	1.20E-10	mr1830_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
vg0414013336	3.45E-09	8.92E-14	mr1846_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
vg0414013336	1.80E-07	3.84E-22	mr1846_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