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Detailed information for vg1203658518:

Variant ID: vg1203658518 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3658518
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTATGAGGCTCTTGCCACTCTTTGGGGTTTTGATGAAAACTGGATGAGGTACTTTGCTAACCTCCATGACTATTCCATTCCTATGCATCATGAGCGGC[A/G]
TCCCCTGTATCTTGATGGCGGCAAGTTGGGCACAACTGAGGGTTTCAAGCCTTTCCATGTCTACCTCAACCGTATCCTGAGAAGGACCCTCACTCCCAAA

Reverse complement sequence

TTTGGGAGTGAGGGTCCTTCTCAGGATACGGTTGAGGTAGACATGGAAAGGCTTGAAACCCTCAGTTGTGCCCAACTTGCCGCCATCAAGATACAGGGGA[T/C]
GCCGCTCATGATGCATAGGAATGGAATAGTCATGGAGGTTAGCAAAGTACCTCATCCAGTTTTCATCAAAACCCCAAAGAGTGGCAAGAGCCTCATAGGT

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	86.20%	13.50%	0.04%	0.25%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.04%	NA
All Japonica	1512	60.40%	38.90%	0.00%	0.66%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.10%	0.60%	0.00%	0.22%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	1.30%	0.00%	0.00%	NA
Temperate Japonica	767	59.60%	39.80%	0.00%	0.65%	NA
Tropical Japonica	504	51.40%	48.40%	0.00%	0.20%	NA
Japonica Intermediate	241	82.20%	16.20%	0.00%	1.66%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	68.90%	30.00%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1203658518	A -> DEL	LOC_Os12g07410.1	N	frameshift_variant	Average:58.465; most accessible tissue: Zhenshan97 young leaf, score: 83.412	N	N	N	N
vg1203658518	A -> G	LOC_Os12g07410.1	missense_variant ; p.His82Arg; MODERATE	nonsynonymous_codon ; H82R	Average:58.465; most accessible tissue: Zhenshan97 young leaf, score: 83.412	unknown	unknown	TOLERATED	0.90

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203658518	NA	3.79E-06	mr1164	Jap_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
vg1203658518	6.66E-06	NA	mr1205	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
vg1203658518	NA	4.54E-06	mr1709	Jap_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
vg1203658518	NA	1.87E-07	mr1748	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
vg1203658518	7.92E-06	NA	mr1775	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