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Detailed information for vg1204287881:

Variant ID: vg1204287881 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4287881
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCTGGCCCAAAATCGGCCGGTGGCCTCCTCCGTTGCTCTCATACGCAGACTTGTGAATTTTGGCCCAGTTCATCATGCCAATTCTGAGTTCTTGGCCCA[G/T]
TCATGCATAAGTCTGATTCTCGACATCGTCCGATTGATTTATCGTCTGAGTTGATGTCGATTCTCCACCACTTTAGGGTTATTCTTTACAAAAGGTTAGT

Reverse complement sequence

ACTAACCTTTTGTAAAGAATAACCCTAAAGTGGTGGAGAATCGACATCAACTCAGACGATAAATCAATCGGACGATGTCGAGAATCAGACTTATGCATGA[C/A]
TGGGCCAAGAACTCAGAATTGGCATGATGAACTGGGCCAAAATTCACAAGTCTGCGTATGAGAGCAACGGAGGAGGCCACCGGCCGATTTTGGGCCAGGA

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	23.80%	1.30%	2.86%	71.96%	NA
All Indica	2759	5.90%	1.70%	3.77%	88.58%	NA
All Japonica	1512	56.10%	0.80%	1.52%	41.60%	NA
Aus	269	25.70%	0.70%	1.49%	72.12%	NA
Indica I	595	7.40%	0.70%	2.18%	89.75%	NA
Indica II	465	7.50%	1.30%	6.45%	84.73%	NA
Indica III	913	1.20%	2.40%	4.49%	91.89%	NA
Indica Intermediate	786	9.30%	2.00%	2.54%	86.13%	NA
Temperate Japonica	767	80.40%	0.10%	0.00%	19.43%	NA
Tropical Japonica	504	28.80%	1.60%	3.57%	66.07%	NA
Japonica Intermediate	241	35.70%	1.20%	2.07%	61.00%	NA
VI/Aromatic	96	13.50%	1.00%	3.12%	82.29%	NA
Intermediate	90	37.80%	0.00%	1.11%	61.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204287881	G -> DEL	N	N	silent_mutation	Average:9.925; most accessible tissue: Callus, score: 26.63	N	N	N	N
vg1204287881	G -> T	LOC_Os12g08440.1	upstream_gene_variant ; 2568.0bp to feature; MODIFIER	silent_mutation	Average:9.925; most accessible tissue: Callus, score: 26.63	N	N	N	N
vg1204287881	G -> T	LOC_Os12g08430.1	intron_variant ; MODIFIER	silent_mutation	Average:9.925; most accessible tissue: Callus, score: 26.63	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204287881	2.50E-06	NA	mr1918	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