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Detailed information for vg0613088823:

Variant ID: vg0613088823 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13088823
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

CCATCTTGTCCCGAAAATTTGGAGAAGTCCGGGACTTTGAACCGATTGGGAAGAGGAACTCTCTCAAACCACTCAGGGTAAGGCTGCCGATACAAGCTTC[C/T]
AGTCTCTTTTGGTTTAAGCCCAAACTGTTCCCTCATTACGTCGGCAATCACATCGGCCCATGGTCGCTGCTGAGCTGCTGCTTGTGGCTGTTGCTGCATG

Reverse complement sequence

CATGCAGCAACAGCCACAAGCAGCAGCTCAGCAGCGACCATGGGCCGATGTGATTGCCGACGTAATGAGGGAACAGTTTGGGCTTAAACCAAAAGAGACT[G/A]
GAAGCTTGTATCGGCAGCCTTACCCTGAGTGGTTTGAGAGAGTTCCTCTTCCCAATCGGTTCAAAGTCCCGGACTTCTCCAAATTTTCGGGACAAGATGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.60%	9.30%	0.06%	0.00%	NA
All Indica	2759	85.70%	14.30%	0.04%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.07%	0.00%	NA
Aus	269	88.80%	10.80%	0.37%	0.00%	NA
Indica I	595	87.10%	12.80%	0.17%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	80.60%	19.40%	0.00%	0.00%	NA
Indica Intermediate	786	82.80%	17.20%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0613088823	C -> T	LOC_Os06g22520.1	missense_variant ; p.Gly391Arg; MODERATE	nonsynonymous_codon ; G391R	Average:47.756; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	benign	0.92	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613088823	NA	1.58E-06	mr1042	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
vg0613088823	NA	7.09E-07	mr1043	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
vg0613088823	NA	3.64E-06	mr1043	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
vg0613088823	NA	6.15E-07	mr1912	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
vg0613088823	NA	5.47E-06	mr1912	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
vg0613088823	NA	9.68E-07	mr1043_2	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
vg0613088823	NA	3.61E-06	mr1291_2	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
vg0613088823	NA	4.68E-06	mr1291_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
vg0613088823	NA	1.49E-06	mr1677_2	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
vg0613088823	3.60E-06	NA	mr1860_2	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
vg0613088823	NA	3.99E-06	mr1860_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