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Detailed information for vg0618348783:

Variant ID: vg0618348783 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18348783
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

AACGGAAGCATCACTGAACTACCGCAACCTAGTCTGAGTCAGCCAAAAGGTGCACCCTGGTCCAAGTCAGGTGAAGAGAAGATTCCATCCGCAACAGGAG[G/A]
TCGAGCCAAGCAGTCCAGAGTGGAGAAGTTTTGCTAGGCAAGTTTGTTATAAAAGACGCAACGGAAGAAGTCAGACAAGAAGAGAAGACCGCCCAACCTA

Reverse complement sequence

TAGGTTGGGCGGTCTTCTCTTCTTGTCTGACTTCTTCCGTTGCGTCTTTTATAACAAACTTGCCTAGCAAAACTTCTCCACTCTGGACTGCTTGGCTCGA[C/T]
CTCCTGTTGCGGATGGAATCTTCTCTTCACCTGACTTGGACCAGGGTGCACCTTTTGGCTGACTCAGACTAGGTTGCGGTAGTTCAGTGATGCTTCCGTT

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	37.70%	10.10%	17.35%	34.79%	NA
All Indica	2759	21.70%	11.30%	15.80%	51.14%	NA
All Japonica	1512	71.10%	0.90%	16.07%	11.90%	NA
Aus	269	25.70%	21.90%	39.03%	13.38%	NA
Indica I	595	42.50%	3.90%	6.05%	47.56%	NA
Indica II	465	23.70%	5.60%	14.62%	56.13%	NA
Indica III	913	4.60%	19.80%	21.47%	54.11%	NA
Indica Intermediate	786	24.70%	10.60%	17.30%	47.46%	NA
Temperate Japonica	767	75.40%	0.00%	10.04%	14.60%	NA
Tropical Japonica	504	62.90%	2.20%	25.79%	9.13%	NA
Japonica Intermediate	241	74.70%	1.20%	14.94%	9.13%	NA
VI/Aromatic	96	5.20%	79.20%	15.62%	0.00%	NA
Intermediate	90	38.90%	18.90%	23.33%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618348783	G -> A	LOC_Os06g31550.1	missense_variant ; p.Gly90Asp; MODERATE	nonsynonymous_codon ; G90N	Average:7.466; most accessible tissue: Minghui63 flower, score: 13.96	possibly damaging	1.839	DELETERIOUS	0.02
vg0618348783	G -> A	LOC_Os06g31550.1	missense_variant ; p.Gly90Asp; MODERATE	nonsynonymous_codon ; G90D	Average:7.466; most accessible tissue: Minghui63 flower, score: 13.96	benign	0.528	TOLERATED	0.33
vg0618348783	G -> DEL	LOC_Os06g31550.1	N	frameshift_variant	Average:7.466; most accessible tissue: Minghui63 flower, score: 13.96	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618348783	1.04E-06	3.49E-06	mr1120	Jap_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
vg0618348783	NA	2.14E-08	mr1570	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