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Detailed information for vg0415096885:

Variant ID: vg0415096885 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 15096885
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATGTTGCAAGGAGGCGACAACTTGGTTTTATAGAGATAACATGACGCGTGATCAGAATGCCTGCACGATCTCCACACCACGTAACCGAACCGGATAAGT[C/T]
ACGCATAACTTATTCGGACTCCACGCCACTTCATGCACCAGATTATTTGATGTATTTCCAAAATCTATGTTTACAAAACAAACACCGAATTTTACAACAA

Reverse complement sequence

TTGTTGTAAAATTCGGTGTTTGTTTTGTAAACATAGATTTTGGAAATACATCAAATAATCTGGTGCATGAAGTGGCGTGGAGTCCGAATAAGTTATGCGT[G/A]
ACTTATCCGGTTCGGTTACGTGGTGTGGAGATCGTGCAGGCATTCTGATCACGCGTCATGTTATCTCTATAAAACCAAGTTGTCGCCTCCTTGCAACATA

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	84.40%	0.30%	0.87%	14.45%	NA
All Indica	2759	88.10%	0.00%	0.40%	11.45%	NA
All Japonica	1512	74.30%	1.00%	1.92%	22.75%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	83.70%	0.00%	0.84%	15.46%	NA
Indica II	465	96.10%	0.00%	0.22%	3.66%	NA
Indica III	913	83.60%	0.00%	0.55%	15.88%	NA
Indica Intermediate	786	92.10%	0.00%	0.00%	7.89%	NA
Temperate Japonica	767	59.20%	1.60%	3.39%	35.85%	NA
Tropical Japonica	504	93.10%	0.00%	0.00%	6.94%	NA
Japonica Intermediate	241	83.40%	1.20%	1.24%	14.11%	NA
VI/Aromatic	96	84.40%	0.00%	1.04%	14.58%	NA
Intermediate	90	90.00%	0.00%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0415096885	C -> DEL	N	N	silent_mutation	Average:35.8; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0415096885	C -> T	LOC_Os04g25960.1	upstream_gene_variant ; 1267.0bp to feature; MODIFIER	silent_mutation	Average:35.8; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0415096885	C -> T	LOC_Os04g25950.1	downstream_gene_variant ; 2203.0bp to feature; MODIFIER	silent_mutation	Average:35.8; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0415096885	C -> T	LOC_Os04g25950-LOC_Os04g25960	intergenic_region ; MODIFIER	silent_mutation	Average:35.8; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0415096885	1.74E-07	NA	mr1300	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
vg0415096885	NA	6.05E-06	mr1300	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
vg0415096885	1.96E-06	NA	mr1310	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
vg0415096885	NA	6.28E-06	mr1837	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
vg0415096885	1.17E-06	NA	mr1926	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
vg0415096885	NA	1.25E-09	mr1959	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