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Detailed information for vg1212722547:

Variant ID: vg1212722547 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 12722547
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, C: 0.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTATTTTCCTATGGGTTATAATTTGACTAGCATGGACCTTATATATTGGATTGGTTCAGCTAGATGTTATTTATAGTTGCTTAGAAACTTGTCAATGGTG[G/C]
GTTGTGAGCACATGGTTTTGAAGGTCGTGCTCATGGCAATTAAAGACAGGTTCGTGAGCTACTGTTGTGAGACATTAACCGTGCCAACCACAAGCCAGCG

Reverse complement sequence

CGCTGGCTTGTGGTTGGCACGGTTAATGTCTCACAACAGTAGCTCACGAACCTGTCTTTAATTGCCATGAGCACGACCTTCAAAACCATGTGCTCACAAC[C/G]
CACCATTGACAAGTTTCTAAGCAACTATAAATAACATCTAGCTGAACCAATCCAATATATAAGGTCCATGCTAGTCAAATTATAACCCATAGGAAAATAA

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	88.20%	11.80%	0.02%	0.00%	NA
All Indica	2759	80.40%	19.60%	0.04%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.20%	1.80%	0.00%	0.00%	NA
Indica II	465	64.90%	35.10%	0.00%	0.00%	NA
Indica III	913	78.40%	21.60%	0.00%	0.00%	NA
Indica Intermediate	786	78.20%	21.60%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg1212722547	G -> C	LOC_Os12g22540.1	missense_variant ; p.Gly3Arg; MODERATE	nonsynonymous_codon ; G3R	Average:46.935; most accessible tissue: Minghui63 panicle, score: 66.554	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1212722547	NA	2.02E-06	mr1425	Ind_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
vg1212722547	NA	3.59E-06	mr1425_2	Ind_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