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Detailed information for vg1210105251:

Variant ID: vg1210105251 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 10105251
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGTGAACGCCGCCCCGTCGGTTTTAGACCCTATTGGATCTATAGGAAGTTGATCAGCAGTGGTATAGGCTTTATCTTTTAATGTGTAATCATCCATAA[G/A]
AGAACCTAGCGTACTCCATAAAAACCCATCAACTTTTTCCTTAAACATCACATCTAATCTATCTTTAAAATTAGCCATAGATGAATCTATTGTATTTGCA

Reverse complement sequence

TGCAAATACAATAGATTCATCTATGGCTAATTTTAAAGATAGATTAGATGTGATGTTTAAGGAAAAAGTTGATGGGTTTTTATGGAGTACGCTAGGTTCT[C/T]
TTATGGATGATTACACATTAAAAGATAAAGCCTATACCACTGCTGATCAACTTCCTATAGATCCAATAGGGTCTAAAACCGACGGGGCGGCGTTCACGGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	29.70%	29.50%	16.72%	24.16%	NA
All Indica	2759	47.00%	6.30%	15.69%	30.99%	NA
All Japonica	1512	1.20%	77.30%	6.68%	14.81%	NA
Aus	269	9.30%	1.50%	73.98%	15.24%	NA
Indica I	595	12.90%	3.20%	17.82%	66.05%	NA
Indica II	465	46.50%	13.80%	13.76%	26.02%	NA
Indica III	913	75.50%	3.80%	11.83%	8.87%	NA
Indica Intermediate	786	40.10%	7.10%	19.72%	33.08%	NA
Temperate Japonica	767	0.50%	87.60%	6.00%	5.87%	NA
Tropical Japonica	504	1.80%	67.10%	6.35%	24.80%	NA
Japonica Intermediate	241	2.10%	66.00%	9.54%	22.41%	NA
VI/Aromatic	96	46.90%	7.30%	40.62%	5.21%	NA
Intermediate	90	18.90%	42.20%	20.00%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1210105251	G -> DEL	LOC_Os12g17640.1	N	frameshift_variant	Average:44.233; most accessible tissue: Minghui63 young leaf, score: 82.368	N	N	N	N
vg1210105251	G -> A	LOC_Os12g17640.1	missense_variant ; p.Leu116Phe; MODERATE	nonsynonymous_codon ; L116F	Average:44.233; most accessible tissue: Minghui63 young leaf, score: 82.368	unknown	unknown	TOLERATED	0.27

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1210105251	2.86E-06	2.86E-06	mr1012	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