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Detailed information for vg0429135610:

Variant ID: vg0429135610 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 29135610
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTGACAAATCAGTTTTATTTGTTATTGATAACTAATATTTTTTTTACTTTTAACTCGATTGTTAAAAAATTATTAAAAGTTAGTAATTTTCGCAATAA[A/T]
GCGCGGAGAATCACCTAATATTCCGGAAAGAGAAGAACAGAGCATCGTATGTGGTCTGTGGTTCGGTTTGGGTTGGAATGCATACTACTAACGTTTAACT

Reverse complement sequence

AGTTAAACGTTAGTAGTATGCATTCCAACCCAAACCGAACCACAGACCACATACGATGCTCTGTTCTTCTCTTTCCGGAATATTAGGTGATTCTCCGCGC[T/A]
TTATTGCGAAAATTACTAACTTTTAATAATTTTTTAACAATCGAGTTAAAAGTAAAAAAAATATTAGTTATCAATAACAAATAAAACTGATTTGTCAAAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.10%	1.70%	0.99%	0.21%	NA
All Indica	2759	99.70%	0.00%	0.18%	0.14%	NA
All Japonica	1512	92.50%	4.60%	2.65%	0.33%	NA
Aus	269	98.90%	0.00%	0.74%	0.37%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.00%	0.00%	0.22%	NA
Indica Intermediate	786	99.10%	0.00%	0.64%	0.25%	NA
Temperate Japonica	767	87.90%	7.40%	4.56%	0.13%	NA
Tropical Japonica	504	99.00%	0.40%	0.00%	0.60%	NA
Japonica Intermediate	241	93.40%	4.10%	2.07%	0.41%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0429135610	A -> DEL	N	N	silent_mutation	Average:33.915; most accessible tissue: Callus, score: 49.201	N	N	N	N
vg0429135610	A -> T	LOC_Os04g48850.1	upstream_gene_variant ; 928.0bp to feature; MODIFIER	silent_mutation	Average:33.915; most accessible tissue: Callus, score: 49.201	N	N	N	N
vg0429135610	A -> T	LOC_Os04g48850-LOC_Os04g48870	intergenic_region ; MODIFIER	silent_mutation	Average:33.915; most accessible tissue: Callus, score: 49.201	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0429135610	6.15E-06	6.15E-06	mr1191	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
vg0429135610	1.47E-08	1.47E-08	mr1644	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