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Detailed information for vg1218430770:

Variant ID: vg1218430770 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18430770
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, C: 0.10, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GCCTTCTCCTTCTCCAGTTCGGCCTTGAGGCGATCAACCTCGGCCCAGGCATCTTTCCCCTTGTCCAGTTCGGACTGAAGGCGTTTGACTTCAGTTTTCG[G/C]
CTCCTTGAGGGTGTGGGCCAGGGACTCCACCTCCAAGTTCTTGCGGCTTATTTCATCATCCTTGGCCCGAAGACGGCTCTTAAAACCGTCAAAACGGGCC

Reverse complement sequence

GGCCCGTTTTGACGGTTTTAAGAGCCGTCTTCGGGCCAAGGATGATGAAATAAGCCGCAAGAACTTGGAGGTGGAGTCCCTGGCCCACACCCTCAAGGAG[C/G]
CGAAAACTGAAGTCAAACGCCTTCAGTCCGAACTGGACAAGGGGAAAGATGCCTGGGCCGAGGTTGATCGCCTCAAGGCCGAACTGGAGAAGGAGAAGGC

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	49.20%	21.30%	2.26%	27.23%	NA
All Indica	2759	23.90%	35.50%	2.46%	38.13%	NA
All Japonica	1512	97.60%	0.70%	0.26%	1.46%	NA
Aus	269	15.20%	2.20%	7.43%	75.09%	NA
Indica I	595	40.20%	22.20%	2.86%	34.79%	NA
Indica II	465	27.30%	21.30%	3.23%	48.17%	NA
Indica III	913	10.60%	53.20%	1.86%	34.28%	NA
Indica Intermediate	786	24.90%	33.50%	2.42%	39.19%	NA
Temperate Japonica	767	98.60%	0.30%	0.00%	1.17%	NA
Tropical Japonica	504	98.80%	0.40%	0.40%	0.40%	NA
Japonica Intermediate	241	92.10%	2.50%	0.83%	4.56%	NA
VI/Aromatic	96	82.30%	2.10%	13.54%	2.08%	NA
Intermediate	90	75.60%	12.20%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218430770	G -> C	LOC_Os12g30690.1	missense_variant ; p.Pro599Ala; MODERATE	nonsynonymous_codon ; P599A	Average:32.917; most accessible tissue: Zhenshan97 flag leaf, score: 72.387	unknown	unknown	TOLERATED	1.00
vg1218430770	G -> DEL	LOC_Os12g30690.1	N	frameshift_variant	Average:32.917; most accessible tissue: Zhenshan97 flag leaf, score: 72.387	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218430770	1.19E-06	1.19E-06	mr1473	Ind_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
vg1218430770	NA	7.58E-08	mr1659	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
vg1218430770	7.48E-06	NA	mr1659	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