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Detailed information for vg0318243134:

Variant ID: vg0318243134 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18243134
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:

TGTCCGAATGATTGTATCCTATATCGCGGTGAGGAGTACGAGAACCTAGAAGCATGCCCTGTTTGTAAAGCACTACGATACAAGATTAGACGAGACGATC[C/T]
AGGAGAAGTTGATGGGCAGCTAACAAAGAAGAGAATTCCTGCTAAGGTGATGTGGTATTTCCCTATAATACCACGGCTAAGGCGTTTGTTCAGGAACAAG

Reverse complement sequence

CTTGTTCCTGAACAAACGCCTTAGCCGTGGTATTATAGGGAAATACCACATCACCTTAGCAGGAATTCTCTTCTTTGTTAGCTGCCCATCAACTTCTCCT[G/A]
GATCGTCTCGTCTAATCTTGTATCGTAGTGCTTTACAAACAGGGCATGCTTCTAGGTTCTCGTACTCCTCACCGCGATATAGGATACAATCATTCGGACA

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	89.50%	9.10%	1.40%	0.00%	NA
All Indica	2759	82.60%	15.20%	2.25%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	88.60%	6.90%	4.54%	0.00%	NA
Indica II	465	97.60%	1.30%	1.08%	0.00%	NA
Indica III	913	71.70%	28.00%	0.22%	0.00%	NA
Indica Intermediate	786	81.80%	14.60%	3.56%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	5.60%	3.33%	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
vg0318243134	C -> T	LOC_Os03g31890.1	missense_variant ; p.Pro164Leu; MODERATE	nonsynonymous_codon ; P164L	Average:22.038; most accessible tissue: Minghui63 panicle, score: 34.226	benign	0.584	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318243134	NA	1.23E-07	mr1221	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
vg0318243134	NA	2.01E-09	mr1739	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
vg0318243134	NA	9.89E-07	mr1043_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
vg0318243134	NA	3.03E-06	mr1043_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
vg0318243134	NA	4.90E-06	mr1269_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
vg0318243134	NA	7.81E-06	mr1502_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
vg0318243134	NA	2.51E-06	mr1677_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
vg0318243134	4.81E-06	2.19E-06	mr1912_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
vg0318243134	1.87E-06	1.87E-06	mr1912_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