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Detailed information for vg1220182193:

Variant ID: vg1220182193 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20182193
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

GTACGGGATATTTTTGGCCGACAATGTTGGAAGATTGTTTCAGATATTACAAGGGTTGTCAAGATTATCAGAAATTTAGTGCAATTCAGAGAGCGCCAGC[G/A]
TCGGCTATGAATCCTATCATTAAACCGTGGCCATTCAGAGGATGGGGAATTGATATGATCGGCATGATTAATCCACCATCGAGTAAAGGACATAAGTTTA

Reverse complement sequence

TAAACTTATGTCCTTTACTCGATGGTGGATTAATCATGCCGATCATATCAATTCCCCATCCTCTGAATGGCCACGGTTTAATGATAGGATTCATAGCCGA[C/T]
GCTGGCGCTCTCTGAATTGCACTAAATTTCTGATAATCTTGACAACCCTTGTAATATCTGAAACAATCTTCCAACATTGTCGGCCAAAAATATCCCGTAC

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	83.50%	7.80%	4.89%	3.83%	NA
All Indica	2759	74.20%	12.70%	7.79%	5.33%	NA
All Japonica	1512	96.20%	1.00%	0.66%	2.12%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	92.40%	3.20%	3.19%	1.18%	NA
Indica II	465	63.00%	17.20%	10.11%	9.68%	NA
Indica III	913	70.50%	16.10%	8.54%	4.82%	NA
Indica Intermediate	786	71.10%	13.40%	9.03%	6.49%	NA
Temperate Japonica	767	97.50%	0.30%	0.26%	1.96%	NA
Tropical Japonica	504	94.20%	2.40%	0.99%	2.38%	NA
Japonica Intermediate	241	96.30%	0.40%	1.24%	2.07%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	93.30%	1.10%	4.44%	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
vg1220182193	G -> DEL	LOC_Os12g33370.1	N	frameshift_variant	Average:21.17; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1220182193	G -> A	LOC_Os12g33370.1	synonymous_variant ; p.Ala287Ala; LOW	synonymous_codon	Average:21.17; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220182193	2.47E-06	NA	mr1237	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