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Detailed information for vg1217812137:

Variant ID: vg1217812137 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17812137
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAAATTCTGTTGCAGCTTAAACAAAATAGCACCCAAGAAACCTCACCGGTGCTGAAGCCAATGAACATTTTCTCGAGACCCAAAGACATGTCCTTGTA[G/A]
TTCTTGTAAGTTTTGAGGTCCACCGTCCTCAGATATGGTGCACCATCCATGCTAACCGTCATGTTCATCTGCGTCGACTCCGGTCACCAACACAAGGTGA

Reverse complement sequence

TCACCTTGTGTTGGTGACCGGAGTCGACGCAGATGAACATGACGGTTAGCATGGATGGTGCACCATATCTGAGGACGGTGGACCTCAAAACTTACAAGAA[C/T]
TACAAGGACATGTCTTTGGGTCTCGAGAAAATGTTCATTGGCTTCAGCACCGGTGAGGTTTCTTGGGTGCTATTTTGTTTAAGCTGCAACAGAATTTAAA

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	60.20%	5.10%	0.34%	34.43%	NA
All Indica	2759	57.10%	8.30%	0.40%	34.18%	NA
All Japonica	1512	69.60%	0.10%	0.20%	30.03%	NA
Aus	269	43.90%	0.70%	0.37%	55.02%	NA
Indica I	595	85.40%	6.20%	0.17%	8.24%	NA
Indica II	465	39.10%	3.90%	0.65%	56.34%	NA
Indica III	913	49.30%	8.40%	0.22%	42.06%	NA
Indica Intermediate	786	55.50%	12.30%	0.64%	31.55%	NA
Temperate Japonica	767	95.80%	0.10%	0.00%	4.04%	NA
Tropical Japonica	504	40.10%	0.00%	0.40%	59.52%	NA
Japonica Intermediate	241	48.10%	0.40%	0.41%	51.04%	NA
VI/Aromatic	96	38.50%	1.00%	0.00%	60.42%	NA
Intermediate	90	65.60%	6.70%	1.11%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217812137	G -> DEL	LOC_Os12g29800.1	N	frameshift_variant	Average:18.047; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N
vg1217812137	G -> A	LOC_Os12g29800.1	synonymous_variant ; p.Asn21Asn; LOW	synonymous_codon	Average:18.047; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217812137	4.08E-06	NA	mr1772	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
vg1217812137	2.72E-06	3.52E-06	mr1772	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