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Detailed information for vg1224680477:

Variant ID: vg1224680477 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24680477
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTCGATCTCGGTTCAAAACTGTAGAGACAGGAAGTTATCGACAACGCTAGAGGGAGTCCAACAGTTCGAATATGAATTTAAATTGAAGTCTGAACAACC[G/A]
CCCTTAACAGGCTCCTTGAATTTTCGGCGACAATCTCTCTCCTTCCTTAGAATACGAACCGTCAGATAGTGCGCCAATTTAAAGGGATTTTGGGATACAT

Reverse complement sequence

ATGTATCCCAAAATCCCTTTAAATTGGCGCACTATCTGACGGTTCGTATTCTAAGGAAGGAGAGAGATTGTCGCCGAAAATTCAAGGAGCCTGTTAAGGG[C/T]
GGTTGTTCAGACTTCAATTTAAATTCATATTCGAACTGTTGGACTCCCTCTAGCGTTGTCGATAACTTCCTGTCTCTACAGTTTTGAACCGAGATCGACC

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	89.90%	9.80%	0.04%	0.30%	NA
All Indica	2759	99.40%	0.10%	0.00%	0.51%	NA
All Japonica	1512	75.00%	24.90%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.60%	0.00%	0.00%	1.42%	NA
Indica Intermediate	786	99.70%	0.10%	0.00%	0.13%	NA
Temperate Japonica	767	85.80%	14.10%	0.13%	0.00%	NA
Tropical Japonica	504	74.40%	25.40%	0.20%	0.00%	NA
Japonica Intermediate	241	41.90%	58.10%	0.00%	0.00%	NA
VI/Aromatic	96	21.90%	78.10%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg1224680477	G -> DEL	N	N	silent_mutation	Average:49.198; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1224680477	G -> A	LOC_Os12g39940.1	upstream_gene_variant ; 3836.0bp to feature; MODIFIER	silent_mutation	Average:49.198; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1224680477	G -> A	LOC_Os12g39930.1	downstream_gene_variant ; 1173.0bp to feature; MODIFIER	silent_mutation	Average:49.198; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1224680477	G -> A	LOC_Os12g39920-LOC_Os12g39930	intergenic_region ; MODIFIER	silent_mutation	Average:49.198; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224680477	4.56E-06	NA	mr1648	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
vg1224680477	6.49E-06	NA	mr1648	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