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Detailed information for vg0412455905:

Variant ID: vg0412455905 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12455905
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

AGGGTCTCCCCGCGCCAAGAGGAGTCCTGATCCGCACCACGCCCGGCAAGTCGACGACGGCACCCGTGTGCATTCAACTTGCGCCCAGGAACCCACCTCC[G/A]
CCTGCAGCTCCCGCAGCTCCTCCAGTTCTGCCCCACAGTTGCCGCAGCTCCTGCAGCTCCAGAGCCAGTCCCAGCTCATGTTCCAGTGTCAGCTCCCGTG

Reverse complement sequence

CACGGGAGCTGACACTGGAACATGAGCTGGGACTGGCTCTGGAGCTGCAGGAGCTGCGGCAACTGTGGGGCAGAACTGGAGGAGCTGCGGGAGCTGCAGG[C/T]
GGAGGTGGGTTCCTGGGCGCAAGTTGAATGCACACGGGTGCCGTCGTCGACTTGCCGGGCGTGGTGCGGATCAGGACTCCTCTTGGCGCGGGGAGACCCT

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	79.90%	6.50%	10.56%	3.00%	NA
All Indica	2759	71.10%	10.60%	16.67%	1.56%	NA
All Japonica	1512	99.30%	0.60%	0.00%	0.07%	NA
Aus	269	52.00%	1.10%	11.15%	35.69%	NA
Indica I	595	74.10%	3.00%	22.18%	0.67%	NA
Indica II	465	61.30%	20.90%	16.99%	0.86%	NA
Indica III	913	73.70%	9.70%	15.01%	1.53%	NA
Indica Intermediate	786	71.80%	11.30%	14.25%	2.67%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.00%	1.80%	0.00%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	0.00%	4.17%	1.04%	NA
Intermediate	90	88.90%	4.40%	5.56%	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
vg0412455905	G -> DEL	LOC_Os04g22000.1	N	frameshift_variant	Average:24.273; most accessible tissue: Callus, score: 35.944	N	N	N	N
vg0412455905	G -> A	LOC_Os04g22000.1	synonymous_variant ; p.Pro210Pro; LOW	synonymous_codon	Average:24.273; most accessible tissue: Callus, score: 35.944	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412455905	8.20E-07	2.53E-11	mr1053	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
vg0412455905	1.70E-07	1.89E-08	mr1053	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
vg0412455905	8.73E-06	NA	mr1070	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
vg0412455905	5.63E-07	5.25E-07	mr1070	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
vg0412455905	9.19E-06	1.55E-06	mr1076	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
vg0412455905	3.51E-06	5.28E-07	mr1128	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
vg0412455905	NA	1.64E-06	mr1139	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
vg0412455905	NA	3.68E-06	mr1145	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
vg0412455905	1.42E-07	3.16E-08	mr1147	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
vg0412455905	NA	1.30E-06	mr1204	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
vg0412455905	NA	8.61E-06	mr1252	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
vg0412455905	NA	8.92E-06	mr1433	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
vg0412455905	NA	5.84E-06	mr1436	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
vg0412455905	NA	2.00E-07	mr1437	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
vg0412455905	NA	3.30E-09	mr1709	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
vg0412455905	NA	5.00E-08	mr1709	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
vg0412455905	NA	7.99E-07	mr1027_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
vg0412455905	4.65E-06	3.20E-09	mr1053_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
vg0412455905	NA	6.43E-07	mr1053_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
vg0412455905	6.94E-06	NA	mr1147_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
vg0412455905	NA	2.42E-06	mr1147_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
vg0412455905	NA	3.57E-06	mr1250_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