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Detailed information for vg0909288154:

Variant ID: vg0909288154 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9288154
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGATGACATATATATAGGAGATGCATCTGTCAAACTACTAGAAAACTGATCTTTGCAGGGTTGGCCGAAAACTACAATAGTTCCGGTTCCAATAAAAACC[G/A]
GGACAAAAAAATAATTTTTAGTCCCGATTAAAAGCTATGTAATCTTTATTACCAACCGGGACTAAAGATCATCCTATGTTAGTGGCCTGTCGGTGGGCCG

Reverse complement sequence

CGGCCCACCGACAGGCCACTAACATAGGATGATCTTTAGTCCCGGTTGGTAATAAAGATTACATAGCTTTTAATCGGGACTAAAAATTATTTTTTTGTCC[C/T]
GGTTTTTATTGGAACCGGAACTATTGTAGTTTTCGGCCAACCCTGCAAAGATCAGTTTTCTAGTAGTTTGACAGATGCATCTCCTATATATATGTCATCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.60%	10.30%	0.87%	2.18%	NA
All Indica	2759	95.50%	2.60%	0.25%	1.56%	NA
All Japonica	1512	81.00%	17.40%	1.59%	0.07%	NA
Aus	269	45.40%	53.90%	0.37%	0.37%	NA
Indica I	595	95.50%	4.20%	0.00%	0.34%	NA
Indica II	465	98.10%	0.20%	0.43%	1.29%	NA
Indica III	913	97.20%	1.10%	0.22%	1.53%	NA
Indica Intermediate	786	92.20%	4.70%	0.38%	2.67%	NA
Temperate Japonica	767	88.30%	11.20%	0.52%	0.00%	NA
Tropical Japonica	504	78.60%	17.70%	3.77%	0.00%	NA
Japonica Intermediate	241	62.70%	36.50%	0.41%	0.41%	NA
VI/Aromatic	96	38.50%	1.00%	6.25%	54.17%	NA
Intermediate	90	83.30%	6.70%	3.33%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909288154	G -> DEL	N	N	silent_mutation	Average:44.099; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0909288154	G -> A	LOC_Os09g15260.1	downstream_gene_variant ; 4118.0bp to feature; MODIFIER	silent_mutation	Average:44.099; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0909288154	G -> A	LOC_Os09g15260-LOC_Os09g15270	intergenic_region ; MODIFIER	silent_mutation	Average:44.099; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909288154	NA	2.44E-11	mr1180	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
vg0909288154	NA	2.15E-08	mr1465	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
vg0909288154	NA	7.75E-16	mr1180_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
vg0909288154	NA	1.14E-07	mr1215_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
vg0909288154	NA	5.16E-10	mr1228_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
vg0909288154	4.43E-07	NA	mr1550_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
vg0909288154	NA	4.00E-15	mr1583_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
vg0909288154	NA	4.61E-07	mr1597_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
vg0909288154	NA	7.41E-08	mr1702_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
vg0909288154	NA	3.87E-07	mr1702_2	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
vg0909288154	NA	1.46E-09	mr1705_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
vg0909288154	NA	8.47E-09	mr1707_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
vg0909288154	NA	6.86E-09	mr1729_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
vg0909288154	NA	5.12E-10	mr1740_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
vg0909288154	NA	2.26E-09	mr1741_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
vg0909288154	NA	6.21E-09	mr1829_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