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Detailed information for vg1226730127:

Variant ID: vg1226730127 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 26730127
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, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GGGCCGAAGCTCGCCTAGATCTTCGAGTGGGAGATGTCCTGACTGTGAAGACAGCGGCCAAATCATCAGGAAGTTTCATCAGGATTGAGGGATAGGACCC[G/A]
TCGTCTTGATCTGGTCGCGGAAGAGTAGATTGGATCTTATCCGAGTGGTTTGAAGCCGACTCGGGAGAGATGATCTTGGAGTAGGCCTCGGCCGAGTTCG

Reverse complement sequence

CGAACTCGGCCGAGGCCTACTCCAAGATCATCTCTCCCGAGTCGGCTTCAAACCACTCGGATAAGATCCAATCTACTCTTCCGCGACCAGATCAAGACGA[C/T]
GGGTCCTATCCCTCAATCCTGATGAAACTTCCTGATGATTTGGCCGCTGTCTTCACAGTCAGGACATCTCCCACTCGAAGATCTAGGCGAGCTTCGGCCC

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	49.80%	2.50%	14.30%	33.45%	NA
All Indica	2759	21.00%	4.20%	18.45%	56.40%	NA
All Japonica	1512	99.70%	0.10%	0.13%	0.13%	NA
Aus	269	43.90%	0.00%	55.02%	1.12%	NA
Indica I	595	44.50%	14.30%	20.34%	20.84%	NA
Indica II	465	9.20%	0.40%	13.55%	76.77%	NA
Indica III	913	14.10%	0.00%	17.96%	67.91%	NA
Indica Intermediate	786	18.10%	3.60%	20.48%	57.89%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	0.40%	0.41%	0.41%	NA
VI/Aromatic	96	90.60%	0.00%	7.29%	2.08%	NA
Intermediate	90	68.90%	0.00%	11.11%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1226730127	G -> DEL	LOC_Os12g43034.1	N	frameshift_variant	Average:30.888; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N
vg1226730127	G -> A	LOC_Os12g43034.1	synonymous_variant ; p.Asp169Asp; LOW	synonymous_codon	Average:30.888; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1226730127	1.57E-06	NA	mr1754_2	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