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Detailed information for vg0308448402:

Variant ID: vg0308448402 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 8448402
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTGAGTTTTTGCCTTGCAACGTTTAACCACTCGTCTTATTCAAAATTTTTTGAAATTATTAATTATTTTATTTGTGACTTACTTTATTATCTACAGTA[C/T,A]
TTTAAGCACAACTTTTTATTTTTTATATCTGCAAAAAAAAATTGAATAAGACGAGTGGTCTAACGTTATAAGCAAAAACTGAAAATCTCTATATTGTGGG

Reverse complement sequence

CCCACAATATAGAGATTTTCAGTTTTTGCTTATAACGTTAGACCACTCGTCTTATTCAATTTTTTTTTGCAGATATAAAAAATAAAAAGTTGTGCTTAAA[G/A,T]
TACTGTAGATAATAAAGTAAGTCACAAATAAAATAATTAATAATTTCAAAAAATTTTGAATAAGACGAGTGGTTAAACGTTGCAAGGCAAAAACTCAAAA

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	79.90%	19.60%	0.25%	0.21%	A: 0.04%
All Indica	2759	79.40%	20.20%	0.29%	0.07%	NA
All Japonica	1512	99.10%	0.90%	0.07%	0.00%	NA
Aus	269	4.50%	92.90%	0.74%	1.86%	NA
Indica I	595	87.40%	12.60%	0.00%	0.00%	NA
Indica II	465	37.40%	61.30%	1.29%	0.00%	NA
Indica III	913	97.40%	2.30%	0.22%	0.11%	NA
Indica Intermediate	786	77.50%	22.40%	0.00%	0.13%	NA
Temperate Japonica	767	99.00%	1.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	80.20%	0.00%	3.12%	NA
Intermediate	90	66.70%	30.00%	1.11%	0.00%	A: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0308448402	C -> T	LOC_Os03g15430-LOC_Os03g15440	intergenic_region ; MODIFIER	silent_mutation	Average:26.559; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0308448402	C -> A	LOC_Os03g15430-LOC_Os03g15440	intergenic_region ; MODIFIER	silent_mutation	Average:26.559; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0308448402	C -> DEL	N	N	silent_mutation	Average:26.559; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0308448402	NA	1.26E-14	mr1522	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
vg0308448402	NA	2.78E-17	mr1557	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
vg0308448402	NA	1.18E-18	mr1715	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
vg0308448402	NA	3.65E-08	mr1806	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
vg0308448402	3.38E-06	1.21E-11	mr1522_2	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
vg0308448402	NA	1.47E-06	mr1574_2	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
vg0308448402	NA	4.31E-18	mr1715_2	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