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Detailed information for vg0500246375:

Variant ID: vg0500246375 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 246375
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.04, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

TAGAGGAAGTTCTCTTGTATTCTTCTGCGCCTAATAAAGGCTGACTGTGCAGGCCCGATCAATTCATCCATTCTCGGGGCGAGACGAAGTGCTAGAATTT[T/C]
GGTCAGGATCTTGGCGAAACTGTGAATCAAACTAATTGGGCAAAAGTCAGTTAGTTGATTCGGGTCCTCTTTCTTGGGCAGGAGGATGATGGAAGCTGTG

Reverse complement sequence

CACAGCTTCCATCATCCTCCTGCCCAAGAAAGAGGACCCGAATCAACTAACTGACTTTTGCCCAATTAGTTTGATTCACAGTTTCGCCAAGATCCTGACC[A/G]
AAATTCTAGCACTTCGTCTCGCCCCGAGAATGGATGAATTGATCGGGCCTGCACAGTCAGCCTTTATTAGGCGCAGAAGAATACAAGAGAACTTCCTCTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.80%	15.20%	0.06%	0.00%	NA
All Indica	2759	80.10%	19.80%	0.11%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	40.50%	59.50%	0.00%	0.00%	NA
Indica I	595	94.10%	5.90%	0.00%	0.00%	NA
Indica II	465	87.70%	12.00%	0.22%	0.00%	NA
Indica III	913	69.10%	30.80%	0.11%	0.00%	NA
Indica Intermediate	786	77.70%	22.10%	0.13%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0500246375	T -> C	LOC_Os05g01420.1	missense_variant ; p.Lys427Glu; MODERATE	nonsynonymous_codon ; K427E	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	unknown	unknown	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0500246375	2.79E-06	7.30E-10	mr1531_2	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
vg0500246375	NA	9.96E-06	mr1624_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
vg0500246375	NA	9.08E-06	mr1740_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