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Detailed information for vg0412476851:

Variant ID: vg0412476851 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12476851
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTTCGTGCTAGTTGCAATGGGTTACTTCACTAAGTGAGCCGAAGCCGTGCCGCTCGAGAATATTACTACGGAGGTAATTGGCTTTATTTTGAAGCATAT[C/T]
GTTCATAGATTCGGTATTCCTCAAACATTAAAGGAGCTTCTTTTATGTCCAAGGAAGTGAGAAGTTTTGCCGAATCTTATGATATTAAGTTGTTGAGTTC

Reverse complement sequence

GAACTCAACAACTTAATATCATAAGATTCGGCAAAACTTCTCACTTCCTTGGACATAAAAGAAGCTCCTTTAATGTTTGAGGAATACCGAATCTATGAAC[G/A]
ATATGCTTCAAAATAAAGCCAATTACCTCCGTAGTAATATTCTCGAGCGGCACGGCTTCGGCTCACTTAGTGAAGTAACCCATTGCAACTAGCACGAACC

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	93.40%	1.10%	5.35%	0.17%	NA
All Indica	2759	94.40%	0.60%	4.93%	0.11%	NA
All Japonica	1512	99.70%	0.00%	0.13%	0.13%	NA
Aus	269	46.50%	13.00%	39.41%	1.12%	NA
Indica I	595	95.30%	0.00%	4.71%	0.00%	NA
Indica II	465	97.20%	0.60%	1.94%	0.22%	NA
Indica III	913	94.10%	0.70%	5.15%	0.11%	NA
Indica Intermediate	786	92.40%	0.90%	6.62%	0.13%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	0.00%	0.83%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	1.10%	10.00%	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
vg0412476851	C -> DEL	N	N	silent_mutation	Average:12.418; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0412476851	C -> T	LOC_Os04g22020.1	downstream_gene_variant ; 2577.0bp to feature; MODIFIER	silent_mutation	Average:12.418; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0412476851	C -> T	LOC_Os04g22030.1	intron_variant ; MODIFIER	silent_mutation	Average:12.418; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412476851	NA	1.40E-10	mr1307	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
vg0412476851	8.99E-06	8.99E-06	mr1682	Ind_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
vg0412476851	7.83E-06	NA	mr1754	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
vg0412476851	4.36E-06	6.55E-06	mr1754	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
vg0412476851	NA	3.62E-07	mr1764	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
vg0412476851	NA	1.31E-08	mr1866	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