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Detailed information for vg1224938358:

Variant ID: vg1224938358 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24938358
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGTATGACTTGCCTGTGCCATCACAAGTTGTATTAATTGTTCCAAGATATGTTTTTTCAAATGAGTCTGCTACTGCAGTTGCTGTTCGCCAATGTTTC[G/A]
TTGAGGTGCTTCGCTTTTGCTCTGATCTTCTGACATGTTTAATATTTTACAATTACACTCTCATACCATACTCAGATTTTAGTTTTCATGATTAGGATGA

Reverse complement sequence

TCATCCTAATCATGAAAACTAAAATCTGAGTATGGTATGAGAGTGTAATTGTAAAATATTAAACATGTCAGAAGATCAGAGCAAAAGCGAAGCACCTCAA[C/T]
GAAACATTGGCGAACAGCAACTGCAGTAGCAGACTCATTTGAAAAAACATATCTTGGAACAATTAATACAACTTGTGATGGCACAGGCAAGTCATACAGG

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	91.20%	7.60%	1.21%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	72.60%	23.70%	3.77%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	50.30%	42.40%	7.30%	0.00%	NA
Tropical Japonica	504	98.00%	1.80%	0.20%	0.00%	NA
Japonica Intermediate	241	90.00%	10.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1224938358	G -> A	LOC_Os12g40279.1	missense_variant ; p.Val2356Ile; MODERATE	nonsynonymous_codon ; V2356I	Average:45.675; most accessible tissue: Zhenshan97 young leaf, score: 66.83	unknown	unknown	TOLERATED	0.20
vg1224938358	G -> A	LOC_Os12g40279.2	missense_variant ; p.Val2356Ile; MODERATE	nonsynonymous_codon ; V2356I	Average:45.675; most accessible tissue: Zhenshan97 young leaf, score: 66.83	unknown	unknown	TOLERATED	0.33

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224938358	NA	3.68E-06	mr1445	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
vg1224938358	3.57E-07	3.57E-07	mr1474_2	Jap_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