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Detailed information for vg0413703707:

Variant ID: vg0413703707 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13703707
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAGTAGCCAACAATTATCTGCGAGCCTGAGGAAAATGAGCTGCACTTGCTAATTTGAGTCTAGGTTGTTGCGAGATATGATATAGTAAATAAGAGTTGC[G/T]
ATGATCCTGATCCTAGTTTGACTTGAATTCCGGATGTTTTGTTTTTTTCAAAATGATAAAAATGAGAGTTCCTCATTTGATATAAATTCCTACAGAGCCA

Reverse complement sequence

TGGCTCTGTAGGAATTTATATCAAATGAGGAACTCTCATTTTTATCATTTTGAAAAAAACAAAACATCCGGAATTCAAGTCAAACTAGGATCAGGATCAT[C/A]
GCAACTCTTATTTACTATATCATATCTCGCAACAACCTAGACTCAAATTAGCAAGTGCAGCTCATTTTCCTCAGGCTCGCAGATAATTGTTGGCTACTTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.40%	18.80%	3.49%	32.35%	NA
All Indica	2759	24.80%	22.00%	5.62%	47.55%	NA
All Japonica	1512	91.90%	7.60%	0.07%	0.40%	NA
Aus	269	6.70%	23.00%	2.23%	68.03%	NA
Indica I	595	50.60%	12.90%	3.36%	33.11%	NA
Indica II	465	5.80%	33.50%	10.32%	50.32%	NA
Indica III	913	13.70%	23.00%	4.49%	58.82%	NA
Indica Intermediate	786	29.40%	21.00%	5.85%	43.77%	NA
Temperate Japonica	767	98.70%	1.00%	0.13%	0.13%	NA
Tropical Japonica	504	86.30%	13.30%	0.00%	0.40%	NA
Japonica Intermediate	241	82.20%	16.60%	0.00%	1.24%	NA
VI/Aromatic	96	12.50%	79.20%	0.00%	8.33%	NA
Intermediate	90	44.40%	30.00%	3.33%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0413703707	G -> DEL	N	N	silent_mutation	Average:20.886; most accessible tissue: Callus, score: 54.336	N	N	N	N
vg0413703707	G -> T	LOC_Os04g23960.1	downstream_gene_variant ; 3249.0bp to feature; MODIFIER	silent_mutation	Average:20.886; most accessible tissue: Callus, score: 54.336	N	N	N	N
vg0413703707	G -> T	LOC_Os04g23970.1	downstream_gene_variant ; 781.0bp to feature; MODIFIER	silent_mutation	Average:20.886; most accessible tissue: Callus, score: 54.336	N	N	N	N
vg0413703707	G -> T	LOC_Os04g23980.1	downstream_gene_variant ; 2617.0bp to feature; MODIFIER	silent_mutation	Average:20.886; most accessible tissue: Callus, score: 54.336	N	N	N	N
vg0413703707	G -> T	LOC_Os04g23970-LOC_Os04g23980	intergenic_region ; MODIFIER	silent_mutation	Average:20.886; most accessible tissue: Callus, score: 54.336	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413703707	1.28E-12	3.28E-15	mr1350_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
vg0413703707	NA	9.25E-07	mr1730_2	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