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Detailed information for vg0414628053:

Variant ID: vg0414628053 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14628053
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAACAATAACTTTAAACGGGATCAACATGCTCAAAGGGTTGTTTGGGATCTGTGTGACTTGCCTTGCTGGCCTTGGAACTCTTCAAAATCTTCTCCTGC[A/G]
AAAACAGACTCTCCGGAAACGTCGGAATCTAAACAGAAAGGAGCAAAATCACCAAAACAGCACATAAGCAAGCATGAACAGTACATGTGGATATTTTTAA

Reverse complement sequence

TTAAAAATATCCACATGTACTGTTCATGCTTGCTTATGTGCTGTTTTGGTGATTTTGCTCCTTTCTGTTTAGATTCCGACGTTTCCGGAGAGTCTGTTTT[T/C]
GCAGGAGAAGATTTTGAAGAGTTCCAAGGCCAGCAAGGCAAGTCACACAGATCCCAAACAACCCTTTGAGCATGTTGATCCCGTTTAAAGTTATTGTTTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.80%	0.90%	9.44%	0.93%	NA
All Indica	2759	91.20%	1.00%	7.76%	0.00%	NA
All Japonica	1512	95.60%	0.30%	1.26%	2.84%	NA
Aus	269	27.10%	2.20%	70.63%	0.00%	NA
Indica I	595	99.30%	0.20%	0.50%	0.00%	NA
Indica II	465	78.70%	2.20%	19.14%	0.00%	NA
Indica III	913	92.20%	1.20%	6.57%	0.00%	NA
Indica Intermediate	786	91.30%	0.80%	7.89%	0.00%	NA
Temperate Japonica	767	93.50%	0.50%	1.96%	4.04%	NA
Tropical Japonica	504	99.40%	0.20%	0.20%	0.20%	NA
Japonica Intermediate	241	94.20%	0.00%	1.24%	4.56%	NA
VI/Aromatic	96	77.10%	1.00%	20.83%	1.04%	NA
Intermediate	90	95.60%	1.10%	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
vg0414628053	A -> DEL	N	N	silent_mutation	Average:23.869; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0414628053	A -> G	LOC_Os04g25300.1	upstream_gene_variant ; 1474.0bp to feature; MODIFIER	silent_mutation	Average:23.869; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0414628053	A -> G	LOC_Os04g25290.1	downstream_gene_variant ; 4672.0bp to feature; MODIFIER	silent_mutation	Average:23.869; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0414628053	A -> G	LOC_Os04g25310.1	downstream_gene_variant ; 1507.0bp to feature; MODIFIER	silent_mutation	Average:23.869; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0414628053	A -> G	LOC_Os04g25300-LOC_Os04g25310	intergenic_region ; MODIFIER	silent_mutation	Average:23.869; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414628053	NA	1.45E-09	mr1188_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