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Detailed information for vg1220344311:

Variant ID: vg1220344311 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20344311
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

ATATATTCCATGATCCGATCGGCTTGTTGGTTGGGGTTTACATTGATGATGTGGTTGTTAAATCAAAGGAGGTAGAGGACCACATAGCCGATTTGAGGAA[G/A]
GTTTTTGAGAGAACAAGAAAATATGGCTTGAAGATGAATCCCACGAAGTGTGCTTTTGGTGTATCAGCTGGGCAGTTCTTGGGATTTCTTGTTCATGAGA

Reverse complement sequence

TCTCATGAACAAGAAATCCCAAGAACTGCCCAGCTGATACACCAAAAGCACACTTCGTGGGATTCATCTTCAAGCCATATTTTCTTGTTCTCTCAAAAAC[C/T]
TTCCTCAAATCGGCTATGTGGTCCTCTACCTCCTTTGATTTAACAACCACATCATCAATGTAAACCCCAACCAACAAGCCGATCGGATCATGGAATATAT

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	33.70%	2.10%	0.78%	63.35%	NA
All Indica	2759	15.60%	3.60%	1.20%	79.63%	NA
All Japonica	1512	70.60%	0.00%	0.20%	29.17%	NA
Aus	269	15.20%	0.00%	0.00%	84.76%	NA
Indica I	595	38.20%	2.40%	1.01%	58.49%	NA
Indica II	465	13.80%	7.30%	1.51%	77.42%	NA
Indica III	913	2.30%	3.00%	1.31%	93.43%	NA
Indica Intermediate	786	15.00%	3.10%	1.02%	80.92%	NA
Temperate Japonica	767	94.40%	0.00%	0.00%	5.61%	NA
Tropical Japonica	504	31.00%	0.00%	0.40%	68.65%	NA
Japonica Intermediate	241	78.00%	0.00%	0.41%	21.58%	NA
VI/Aromatic	96	12.50%	0.00%	0.00%	87.50%	NA
Intermediate	90	47.80%	2.20%	1.11%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220344311	G -> DEL	LOC_Os12g33700.1	N	frameshift_variant	Average:18.478; most accessible tissue: Callus, score: 68.725	N	N	N	N
vg1220344311	G -> A	LOC_Os12g33700.1	synonymous_variant ; p.Lys72Lys; LOW	synonymous_codon	Average:18.478; most accessible tissue: Callus, score: 68.725	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220344311	NA	4.48E-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
vg1220344311	NA	2.23E-24	mr1588_2	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
vg1220344311	6.83E-06	3.30E-07	mr1588_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
vg1220344311	NA	1.37E-07	mr1804_2	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
vg1220344311	NA	5.00E-09	mr1947_2	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