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Detailed information for vg1112989462:

Variant ID: vg1112989462 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12989462
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTATAGTGGTTTCAGAAAATTCCATAGGCCACATATCAACTCCGATTTAGCTGTAACTTAGAGGTGTGCCTATTTTCGTGTTCTGGAAAAAGAAAAAA[A/T]
TATCAAAAAAATAAAAGAAAAAAAAAGAAAAGTTGATTTCCACTACTGCATTAAGCTCACGACGTGCTCCGTTGAGCTTATCTGCCAGTTCGGTTTTGTT

Reverse complement sequence

AACAAAACCGAACTGGCAGATAAGCTCAACGGAGCACGTCGTGAGCTTAATGCAGTAGTGGAAATCAACTTTTCTTTTTTTTTCTTTTATTTTTTTGATA[T/A]
TTTTTTCTTTTTCCAGAACACGAAAATAGGCACACCTCTAAGTTACAGCTAAATCGGAGTTGATATGTGGCCTATGGAATTTTCTGAAACCACTATAAAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.70%	0.20%	6.50%	17.63%	NA
All Indica	2759	60.60%	0.30%	10.51%	28.56%	NA
All Japonica	1512	97.90%	0.00%	0.53%	1.52%	NA
Aus	269	93.30%	0.00%	2.23%	4.46%	NA
Indica I	595	73.10%	0.20%	9.75%	16.97%	NA
Indica II	465	53.50%	0.00%	9.25%	37.20%	NA
Indica III	913	54.90%	0.70%	12.38%	32.09%	NA
Indica Intermediate	786	62.10%	0.10%	9.67%	28.12%	NA
Temperate Japonica	767	99.60%	0.00%	0.26%	0.13%	NA
Tropical Japonica	504	95.20%	0.00%	0.99%	3.77%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	0.00%	3.33%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112989462	A -> T	LOC_Os11g22580.1	intron_variant ; MODIFIER	silent_mutation	Average:12.433; most accessible tissue: Callus, score: 52.25	N	N	N	N
vg1112989462	A -> DEL	N	N	silent_mutation	Average:12.433; most accessible tissue: Callus, score: 52.25	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112989462	4.05E-06	NA	mr1864	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