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Detailed information for vg0912264986:

Variant ID: vg0912264986 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 12264986
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGACAGATTTGACAGGTGTTTGGTTGTAGCCACAGTTGTGGCAAGATTCCCCTCCAACAAATTGGGTCCCACGTGTCAATGGCTCAAAAAAGTGTGGCAA[G/A]
ATTCCCTTAGACTTAGTAAGTTGTGGCTAACAATTTGATCACCTCACCTTAGGTAAGGTGTGACAACTTTTGTTGGCAAGTAATGGTAAAGTGTGGCTGG

Reverse complement sequence

CCAGCCACACTTTACCATTACTTGCCAACAAAAGTTGTCACACCTTACCTAAGGTGAGGTGATCAAATTGTTAGCCACAACTTACTAAGTCTAAGGGAAT[C/T]
TTGCCACACTTTTTTGAGCCATTGACACGTGGGACCCAATTTGTTGGAGGGGAATCTTGCCACAACTGTGGCTACAACCAAACACCTGTCAAATCTGTCT

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	49.30%	0.80%	10.47%	39.34%	NA
All Indica	2759	18.10%	0.10%	16.46%	65.35%	NA
All Japonica	1512	94.60%	2.40%	0.99%	1.98%	NA
Aus	269	96.30%	0.00%	2.97%	0.74%	NA
Indica I	595	9.20%	0.00%	4.71%	86.05%	NA
Indica II	465	22.40%	0.00%	10.32%	67.31%	NA
Indica III	913	19.50%	0.00%	27.93%	52.57%	NA
Indica Intermediate	786	20.70%	0.30%	15.65%	63.36%	NA
Temperate Japonica	767	92.80%	4.20%	1.30%	1.69%	NA
Tropical Japonica	504	97.00%	0.00%	0.79%	2.18%	NA
Japonica Intermediate	241	95.00%	2.10%	0.41%	2.49%	NA
VI/Aromatic	96	84.40%	0.00%	9.38%	6.25%	NA
Intermediate	90	68.90%	1.10%	10.00%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0912264986	G -> DEL	N	N	silent_mutation	Average:68.774; most accessible tissue: Callus, score: 94.452	N	N	N	N
vg0912264986	G -> A	LOC_Os09g20400.1	intron_variant ; MODIFIER	silent_mutation	Average:68.774; most accessible tissue: Callus, score: 94.452	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0912264986	3.27E-07	3.27E-07	mr1474_2	Jap_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