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Detailed information for vg1222329942:

Variant ID: vg1222329942 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22329942
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGCTCTGCTTTTTGCCGATGAGAAAAAGGTTGTGCTCGTCGGCGGCGGCGAGCTTCTGAAGGATGACGCGGCCCAGCACCATGAGATCCCTGTAGTGA[G/C]
CGGACGGCGCACTGTCTCCGTCTTGCTGCTGCTGTTCCTGCTGCTCCGTGGTGGTGGTGTCGAGCAGCGACGATATGCACGAGAGCGCCTCCGGGAAGCT

Reverse complement sequence

AGCTTCCCGGAGGCGCTCTCGTGCATATCGTCGCTGCTCGACACCACCACCACGGAGCAGCAGGAACAGCAGCAGCAAGACGGAGACAGTGCGCCGTCCG[C/G]
TCACTACAGGGATCTCATGGTGCTGGGCCGCGTCATCCTTCAGAAGCTCGCCGCCGCCGACGAGCACAACCTTTTTCTCATCGGCAAAAAGCAGAGCACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.30%	10.30%	0.55%	4.76%	NA
All Indica	2759	81.90%	15.40%	0.47%	2.21%	NA
All Japonica	1512	96.80%	3.20%	0.00%	0.07%	NA
Aus	269	33.10%	3.70%	4.46%	58.74%	NA
Indica I	595	88.60%	10.90%	0.50%	0.00%	NA
Indica II	465	80.90%	18.50%	0.43%	0.22%	NA
Indica III	913	80.00%	15.20%	0.55%	4.27%	NA
Indica Intermediate	786	79.90%	17.00%	0.38%	2.67%	NA
Temperate Japonica	767	94.00%	6.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.00%	0.41%	NA
VI/Aromatic	96	95.80%	0.00%	1.04%	3.12%	NA
Intermediate	90	90.00%	7.80%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222329942	G -> C	LOC_Os12g36490.1	missense_variant ; p.Ala374Gly; MODERATE	nonsynonymous_codon ; A374G	Average:76.01; most accessible tissue: Zhenshan97 young leaf, score: 91.069	unknown	unknown	TOLERATED	0.51
vg1222329942	G -> DEL	LOC_Os12g36490.1	N	frameshift_variant	Average:76.01; most accessible tissue: Zhenshan97 young leaf, score: 91.069	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222329942	NA	4.16E-06	mr1189	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
vg1222329942	NA	2.02E-06	mr1625	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
vg1222329942	2.30E-06	NA	mr1984	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