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Detailed information for vg1222814459:

Variant ID: vg1222814459 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22814459
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATCAAAGTCGTAAGATAAATCTGTAAGAACTACTATGACCAATTGTAAATAGGTGTCAAAATTAATTGCTATTAATTAAACATCTAATGGCTTGTGAAT[G/T]
GATTTTTAAGATACCTTAACAAAAACTAGAACCCTTAAATTATTACAAAATAACAGTATCCGAACTTTAGTTTGCCCTTAATCTATGAGATAAATTTTTT

Reverse complement sequence

AAAAAATTTATCTCATAGATTAAGGGCAAACTAAAGTTCGGATACTGTTATTTTGTAATAATTTAAGGGTTCTAGTTTTTGTTAAGGTATCTTAAAAATC[C/A]
ATTCACAAGCCATTAGATGTTTAATTAATAGCAATTAATTTTGACACCTATTTACAATTGGTCATAGTAGTTCTTACAGATTTATCTTACGACTTTGATT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.80%	0.10%	3.87%	15.19%	NA
All Indica	2759	67.60%	0.20%	6.49%	25.70%	NA
All Japonica	1512	99.40%	0.00%	0.20%	0.40%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	75.80%	0.20%	3.03%	21.01%	NA
Indica II	465	80.90%	0.00%	7.74%	11.40%	NA
Indica III	913	57.40%	0.00%	7.56%	35.05%	NA
Indica Intermediate	786	65.50%	0.50%	7.12%	26.84%	NA
Temperate Japonica	767	99.50%	0.00%	0.39%	0.13%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	98.90%	0.00%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222814459	G -> DEL	N	N	silent_mutation	Average:22.267; most accessible tissue: Callus, score: 44.412	N	N	N	N
vg1222814459	G -> T	LOC_Os12g37190.1	downstream_gene_variant ; 4741.0bp to feature; MODIFIER	silent_mutation	Average:22.267; most accessible tissue: Callus, score: 44.412	N	N	N	N
vg1222814459	G -> T	LOC_Os12g37200.1	intron_variant ; MODIFIER	silent_mutation	Average:22.267; most accessible tissue: Callus, score: 44.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222814459	3.59E-06	3.59E-06	mr1416_2	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