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Detailed information for vg1217879064:

Variant ID: vg1217879064 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17879064
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAACATTTCTACCTCTTGTGATAATCTTGTGGATATGCCTAGCTCTAGCTCTAGGTCTTGTGTTTCTATTTGTGATGCCTCACTTGTTGTTGAGAACAAT[G/A]
AGCTTAAGGAGCAAGTGGCTAAGCTCAACAAGAGTTTGGAGAGATGCTTCAAGGGTAAGAACACTCTTGACAAGATTTTGAGTGAGCAACGGTGCATCCT

Reverse complement sequence

AGGATGCACCGTTGCTCACTCAAAATCTTGTCAAGAGTGTTCTTACCCTTGAAGCATCTCTCCAAACTCTTGTTGAGCTTAGCCACTTGCTCCTTAAGCT[C/T]
ATTGTTCTCAACAACAAGTGAGGCATCACAAATAGAAACACAAGACCTAGAGCTAGAGCTAGGCATATCCACAAGATTATCACAAGAGGTAGAAATGTTA

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	43.60%	3.80%	10.26%	42.28%	NA
All Indica	2759	42.90%	2.90%	5.33%	48.82%	NA
All Japonica	1512	45.10%	5.70%	18.25%	30.95%	NA
Aus	269	53.50%	1.90%	8.92%	35.69%	NA
Indica I	595	48.70%	1.70%	8.24%	41.34%	NA
Indica II	465	32.30%	0.00%	1.08%	66.67%	NA
Indica III	913	41.20%	4.10%	4.38%	50.38%	NA
Indica Intermediate	786	46.80%	4.30%	6.74%	42.11%	NA
Temperate Japonica	767	76.10%	2.50%	16.43%	4.95%	NA
Tropical Japonica	504	5.00%	10.70%	23.02%	61.31%	NA
Japonica Intermediate	241	30.30%	5.40%	14.11%	50.21%	NA
VI/Aromatic	96	6.20%	2.10%	31.25%	60.42%	NA
Intermediate	90	51.10%	7.80%	8.89%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217879064	G -> DEL	LOC_Os12g29910.1	N	frameshift_variant	Average:8.261; most accessible tissue: Callus, score: 35.175	N	N	N	N
vg1217879064	G -> A	LOC_Os12g29910.1	missense_variant ; p.Glu93Lys; MODERATE	nonsynonymous_codon ; E93K	Average:8.261; most accessible tissue: Callus, score: 35.175	unknown	unknown	TOLERATED	0.13

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217879064	6.45E-07	NA	mr1281_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