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Detailed information for vg0430189232:

Variant ID: vg0430189232 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30189232
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTGTAAGGAGTGTTGTTGGTGCACTTTGTAAACACAGAGAGAATCAATAAAGTCGTCATCCACTTTAAGAGTTCTTCGATTTGTGTTTACCGGGTTTC[G/A]
GCGGTCTAACCGGCGACACACCGGCGGTCAGACCGGCGACACACCGGCGGTCAGACCGGCGGCAATGCGGTGGCAGACCGGCGGCGACAGCAGGCGAGGC

Reverse complement sequence

GCCTCGCCTGCTGTCGCCGCCGGTCTGCCACCGCATTGCCGCCGGTCTGACCGCCGGTGTGTCGCCGGTCTGACCGCCGGTGTGTCGCCGGTTAGACCGC[C/T]
GAAACCCGGTAAACACAAATCGAAGAACTCTTAAAGTGGATGACGACTTTATTGATTCTCTCTGTGTTTACAAAGTGCACCAACAACACTCCTTACAAAA

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	89.40%	1.50%	3.41%	5.78%	NA
All Indica	2759	84.80%	0.10%	5.29%	9.79%	NA
All Japonica	1512	95.40%	3.80%	0.73%	0.07%	NA
Aus	269	97.40%	1.10%	1.12%	0.37%	NA
Indica I	595	82.20%	0.00%	7.56%	10.25%	NA
Indica II	465	78.70%	0.40%	7.96%	12.90%	NA
Indica III	913	92.10%	0.00%	1.20%	6.68%	NA
Indica Intermediate	786	81.80%	0.30%	6.74%	11.20%	NA
Temperate Japonica	767	99.30%	0.50%	0.13%	0.00%	NA
Tropical Japonica	504	87.90%	10.10%	1.98%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0430189232	G -> DEL	N	N	silent_mutation	Average:16.789; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0430189232	G -> A	LOC_Os04g51000.1	upstream_gene_variant ; 3380.0bp to feature; MODIFIER	silent_mutation	Average:16.789; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0430189232	G -> A	LOC_Os04g51000-LOC_Os04g51009	intergenic_region ; MODIFIER	silent_mutation	Average:16.789; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430189232	NA	2.26E-08	mr1248	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
vg0430189232	4.03E-06	8.00E-10	mr1676_2	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