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Detailed information for vg1206837224:

Variant ID: vg1206837224 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6837224
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, C: 0.22, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTCTCTTCTGCTTCCGCTAATACTTCTGTTCCGAACAGTTGACGTTCGCCTGTCTGATCCCAGAAGAGAGGTGTGCGGCACTTCCGGCCGTATAAAGC[C/T]
TCAAATGGTGCCATCTGTAGACTGGCCTGGTAGCTGTTGTTGTACGAGAATTCCGCATATGGCAAGCTTTTGTCCCAAGCTCCACCAAAATCAAGAGCGC

Reverse complement sequence

GCGCTCTTGATTTTGGTGGAGCTTGGGACAAAAGCTTGCCATATGCGGAATTCTCGTACAACAACAGCTACCAGGCCAGTCTACAGATGGCACCATTTGA[G/A]
GCTTTATACGGCCGGAAGTGCCGCACACCTCTCTTCTGGGATCAGACAGGCGAACGTCAACTGTTCGGAACAGAAGTATTAGCGGAAGCAGAAGAGAAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.00%	0.10%	17.58%	55.29%	NA
All Indica	2759	7.80%	0.30%	22.22%	69.74%	NA
All Japonica	1512	57.50%	0.00%	5.75%	36.77%	NA
Aus	269	21.90%	0.00%	45.72%	32.34%	NA
Indica I	595	6.40%	0.00%	15.63%	77.98%	NA
Indica II	465	7.70%	0.00%	24.09%	68.17%	NA
Indica III	913	8.30%	0.70%	23.22%	67.80%	NA
Indica Intermediate	786	8.30%	0.10%	24.94%	66.67%	NA
Temperate Japonica	767	33.80%	0.00%	6.39%	59.84%	NA
Tropical Japonica	504	87.30%	0.00%	3.37%	9.33%	NA
Japonica Intermediate	241	70.50%	0.00%	8.71%	20.75%	NA
VI/Aromatic	96	92.70%	0.00%	3.12%	4.17%	NA
Intermediate	90	47.80%	0.00%	5.56%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206837224	C -> DEL	LOC_Os12g12410.1	N	frameshift_variant	Average:7.759; most accessible tissue: Callus, score: 12.019	N	N	N	N
vg1206837224	C -> T	LOC_Os12g12410.1	synonymous_variant ; p.Glu1288Glu; LOW	synonymous_codon	Average:7.759; most accessible tissue: Callus, score: 12.019	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206837224	1.35E-06	2.17E-07	mr1018	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
vg1206837224	NA	8.33E-07	mr1334	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
vg1206837224	NA	5.79E-11	mr1553	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