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Detailed information for vg0129861515:

Variant ID: vg0129861515 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 29861515
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TCACTTTATATAAAATTGAAAACACATGAGATGAATGTTCTTTCTCGAAAAGTTGATTCTAAGTCGAGTGCTTTGGTTTCTTCTTCTTCCTCTTTGGATG[C/T]
TGATGCTTCTTCATCTAAGTCTTCTTTTCTTGCTGTTTTTAATGCCACATCCGATGATCAACTCGAACAAATCGAGGAGGAGGATTTGGCTTTGGTTGCT

Reverse complement sequence

AGCAACCAAAGCCAAATCCTCCTCCTCGATTTGTTCGAGTTGATCATCGGATGTGGCATTAAAAACAGCAAGAAAAGAAGACTTAGATGAAGAAGCATCA[G/A]
CATCCAAAGAGGAAGAAGAAGAAACCAAAGCACTCGACTTAGAATCAACTTTTCGAGAAAGAACATTCATCTCATGTGTTTTCAATTTTATATAAAGTGA

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	27.40%	10.30%	28.29%	34.00%	NA
All Indica	2759	6.50%	5.50%	34.87%	53.17%	NA
All Japonica	1512	71.40%	1.30%	20.17%	7.21%	NA
Aus	269	0.40%	83.60%	10.04%	5.95%	NA
Indica I	595	4.20%	1.70%	50.25%	43.87%	NA
Indica II	465	10.50%	0.90%	35.05%	53.55%	NA
Indica III	913	3.50%	7.20%	26.51%	62.76%	NA
Indica Intermediate	786	9.20%	9.20%	32.82%	48.85%	NA
Temperate Japonica	767	99.10%	0.10%	0.39%	0.39%	NA
Tropical Japonica	504	21.80%	1.40%	56.94%	19.84%	NA
Japonica Intermediate	241	86.70%	4.60%	6.22%	2.49%	NA
VI/Aromatic	96	3.10%	78.10%	15.62%	3.12%	NA
Intermediate	90	36.70%	18.90%	31.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0129861515	C -> T	LOC_Os01g51950.1	missense_variant ; p.Ala183Val; MODERATE	nonsynonymous_codon ; A183V	Average:14.312; most accessible tissue: Minghui63 young leaf, score: 20.156	benign	-0.674	TOLERATED	1.00
vg0129861515	C -> DEL	LOC_Os01g51950.1	N	frameshift_variant	Average:14.312; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0129861515	NA	2.17E-13	mr1010	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
vg0129861515	6.46E-06	NA	mr1083	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
vg0129861515	NA	5.26E-10	mr1277	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
vg0129861515	NA	4.21E-07	mr1584	Jap_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
vg0129861515	1.10E-06	5.72E-07	mr1720	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
vg0129861515	NA	2.01E-14	mr1740	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
vg0129861515	NA	4.03E-09	mr1746	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
vg0129861515	NA	1.02E-06	mr1748	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
vg0129861515	NA	4.67E-06	mr1837	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
vg0129861515	NA	6.94E-15	mr1982	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
vg0129861515	NA	1.04E-06	mr1097_2	Jap_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
vg0129861515	NA	1.60E-11	mr1520_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
vg0129861515	NA	8.10E-15	mr1539_2	Jap_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