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Detailed information for vg0915452616:

Variant ID: vg0915452616 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 15452616
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGACTAATAACAAAACAAATTACAGACTCCACATGTAAACTGAGACAAATCTATTAAGCCTAATTAATTCATCATTAGTAAATGTTTATTGTAGCACCA[C/T]
ATTGTTAAATCATAACGTAACTAGCATGGTGGCCCGCGCAGATTACGCGGCTAGCATCATTATATTTTCTCTCATATAATAGCATATATGTTTTCTTAAT

Reverse complement sequence

ATTAAGAAAACATATATGCTATTATATGAGAGAAAATATAATGATGCTAGCCGCGTAATCTGCGCGGGCCACCATGCTAGTTACGTTATGATTTAACAAT[G/A]
TGGTGCTACAATAAACATTTACTAATGATGAATTAATTAGGCTTAATAGATTTGTCTCAGTTTACATGTGGAGTCTGTAATTTGTTTTGTTATTAGTCTA

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	67.40%	15.30%	0.11%	17.18%	NA
All Indica	2759	44.90%	25.80%	0.18%	29.07%	NA
All Japonica	1512	99.80%	0.10%	0.00%	0.07%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	23.70%	40.20%	0.50%	35.63%	NA
Indica II	465	66.50%	18.70%	0.00%	14.84%	NA
Indica III	913	44.70%	24.80%	0.00%	30.56%	NA
Indica Intermediate	786	48.50%	20.50%	0.25%	30.79%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	5.60%	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
vg0915452616	C -> DEL	N	N	silent_mutation	Average:29.887; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0915452616	C -> T	LOC_Os09g25770.1	upstream_gene_variant ; 2604.0bp to feature; MODIFIER	silent_mutation	Average:29.887; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0915452616	C -> T	LOC_Os09g25770.2	upstream_gene_variant ; 2604.0bp to feature; MODIFIER	silent_mutation	Average:29.887; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0915452616	C -> T	LOC_Os09g25784.1	intron_variant ; MODIFIER	silent_mutation	Average:29.887; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0915452616	C -> T	LOC_Os09g25784.2	intron_variant ; MODIFIER	silent_mutation	Average:29.887; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0915452616	NA	9.10E-20	mr1598	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
vg0915452616	2.43E-06	7.45E-13	mr1717	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
vg0915452616	4.49E-09	4.49E-09	mr1717	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
vg0915452616	NA	4.44E-10	mr1770	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