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Detailed information for vg1208705079:

Variant ID: vg1208705079 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8705079
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAGGGGAGGAGGATTCGGTCTCTCTCCCTGGTCTCGCACCTCTCTCTGTCGTGTGCCTCTCCCCACCCATCAACGGCGATGGCCCTCCCCACCCAGCT[G/T]
CGGCACCCTCCCACCCGGCGGCGGCAGGGGCGGTGCCTTCCCCGATGTCAGCTCGTTCTTTATATTCTTAGTGTTCTTAGACTTGGATTTTCTTAGCGTA

Reverse complement sequence

TACGCTAAGAAAATCCAAGTCTAAGAACACTAAGAATATAAAGAACGAGCTGACATCGGGGAAGGCACCGCCCCTGCCGCCGCCGGGTGGGAGGGTGCCG[C/A]
AGCTGGGTGGGGAGGGCCATCGCCGTTGATGGGTGGGGAGAGGCACACGACAGAGAGAGGTGCGAGACCAGGGAGAGAGACCGAATCCTCCTCCCCTTAT

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	68.40%	2.50%	0.15%	29.01%	NA
All Indica	2759	59.80%	0.50%	0.18%	39.54%	NA
All Japonica	1512	96.60%	0.00%	0.07%	3.37%	NA
Aus	269	9.70%	26.00%	0.00%	64.31%	NA
Indica I	595	52.80%	0.30%	0.34%	46.55%	NA
Indica II	465	49.90%	0.20%	0.22%	49.68%	NA
Indica III	913	69.70%	0.70%	0.00%	29.68%	NA
Indica Intermediate	786	59.40%	0.60%	0.25%	39.69%	NA
Temperate Japonica	767	94.50%	0.00%	0.13%	5.35%	NA
Tropical Japonica	504	99.00%	0.00%	0.00%	0.99%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	31.20%	26.00%	0.00%	42.71%	NA
Intermediate	90	74.40%	7.80%	1.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208705079	G -> DEL	N	N	silent_mutation	Average:47.52; most accessible tissue: Minghui63 young leaf, score: 71.839	N	N	N	N
vg1208705079	G -> T	LOC_Os12g15250-LOC_Os12g15270	intergenic_region ; MODIFIER	silent_mutation	Average:47.52; most accessible tissue: Minghui63 young leaf, score: 71.839	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208705079	NA	2.55E-07	mr1425	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1208705079	5.21E-07	5.21E-07	mr1529_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
vg1208705079	NA	2.20E-06	mr1864_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251