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Detailed information for vg0332412088:

Variant ID: vg0332412088 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 32412088
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGCATGTCCGCCTTTCGCATCCGCCCGAGGATCAGGGGGAGTCCCAGGTATTTGATCGGGAAGCATGCTCTCACTGCTGGGACTCCCTCTAGGACATC[G/A]
TCCAAATCAATGTTATTGCATTTGATGACCGCGACTTGAGATTTTTGGAAGTTGGTAACGAGTCCAGTAGCCGTGCCGAAACGTTGCAGGATTTCCGTGA

Reverse complement sequence

TCACGGAAATCCTGCAACGTTTCGGCACGGCTACTGGACTCGTTACCAACTTCCAAAAATCTCAAGTCGCGGTCATCAAATGCAATAACATTGATTTGGA[C/T]
GATGTCCTAGAGGGAGTCCCAGCAGTGAGAGCATGCTTCCCGATCAAATACCTGGGACTCCCCCTGATCCTCGGGCGGATGCGAAAGGCGGACATGCAGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.70%	26.90%	4.27%	0.08%	NA
All Indica	2759	47.20%	45.50%	7.14%	0.14%	NA
All Japonica	1512	99.50%	0.40%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	11.30%	74.60%	14.12%	0.00%	NA
Indica II	465	30.80%	61.50%	7.53%	0.22%	NA
Indica III	913	81.80%	16.80%	1.42%	0.00%	NA
Indica Intermediate	786	43.90%	47.50%	8.27%	0.38%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	86.70%	10.00%	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
vg0332412088	G -> A	LOC_Os03g56910.1	synonymous_variant ; p.Asp842Asp; LOW	synonymous_codon	Average:45.551; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N
vg0332412088	G -> DEL	LOC_Os03g56910.1	N	frameshift_variant	Average:45.551; most accessible tissue: Minghui63 young leaf, score: 62.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0332412088	NA	5.83E-08	mr1707	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
vg0332412088	1.77E-06	2.45E-11	mr1860	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