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Detailed information for vg0408392718:

Variant ID: vg0408392718 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8392718
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

TTGACGACGTGATTAGCTTGATTGAGTGCGTCTTCCTTGAGGAGGGTGTCGAGGAGGGTGATCGCTGCAACCGCGTTCTATTGAGGGGTGCGAAAAACCG[C/T]
AGTTCCCTCGATGTCTTGCTGCCCGATAAGCTCTCGTGCTCGTCGCTTGGCGTCCAAGGCCCGTTGCCATCGATCCTCAGCCTCTTTTGCAGCCCGTTCG

Reverse complement sequence

CGAACGGGCTGCAAAAGAGGCTGAGGATCGATGGCAACGGGCCTTGGACGCCAAGCGACGAGCACGAGAGCTTATCGGGCAGCAAGACATCGAGGGAACT[G/A]
CGGTTTTTCGCACCCCTCAATAGAACGCGGTTGCAGCGATCACCCTCCTCGACACCCTCCTCAAGGAAGACGCACTCAATCAAGCTAATCACGTCGTCAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	28.90%	8.30%	4.78%	58.08%	NA
All Indica	2759	9.10%	8.70%	5.29%	76.95%	NA
All Japonica	1512	66.60%	9.00%	2.84%	21.56%	NA
Aus	269	5.90%	0.70%	10.41%	82.90%	NA
Indica I	595	9.40%	1.80%	3.36%	85.38%	NA
Indica II	465	10.80%	4.70%	6.02%	78.49%	NA
Indica III	913	5.50%	16.30%	4.93%	73.27%	NA
Indica Intermediate	786	12.10%	7.30%	6.74%	73.92%	NA
Temperate Japonica	767	96.20%	0.00%	0.52%	3.26%	NA
Tropical Japonica	504	17.10%	25.00%	5.95%	51.98%	NA
Japonica Intermediate	241	75.90%	4.10%	3.73%	16.18%	NA
VI/Aromatic	96	59.40%	5.20%	7.29%	28.12%	NA
Intermediate	90	37.80%	8.90%	2.22%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408392718	C -> DEL	N	N	silent_mutation	Average:17.719; most accessible tissue: Callus, score: 42.38	N	N	N	N
vg0408392718	C -> T	LOC_Os04g14920.1	downstream_gene_variant ; 130.0bp to feature; MODIFIER	silent_mutation	Average:17.719; most accessible tissue: Callus, score: 42.38	N	N	N	N
vg0408392718	C -> T	LOC_Os04g14930.1	downstream_gene_variant ; 3042.0bp to feature; MODIFIER	silent_mutation	Average:17.719; most accessible tissue: Callus, score: 42.38	N	N	N	N
vg0408392718	C -> T	LOC_Os04g14900-LOC_Os04g14920	intergenic_region ; MODIFIER	silent_mutation	Average:17.719; most accessible tissue: Callus, score: 42.38	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408392718	NA	3.07E-09	mr1583	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
vg0408392718	2.67E-06	1.75E-07	mr1835	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