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Detailed information for vg0212831375:

Variant ID: vg0212831375 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 12831375
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCTACACCACCACCCTCCCCTTCTCAACAGCCTGCTCTCCCGGCTCCGCAACCAGTTTAAGCCTCTCCCACCTCCCCAGCTAAACAACATGCTCCCCCG[A/G]
CTCCGCCCTCAGTGCAAGCCTCTCCACCTACACTCCAATCTGCTCTGGTAGAACAAGTGCACATACCAGAAGGTACTACATCCGAACCGAAGTCTAATCC

Reverse complement sequence

GGATTAGACTTCGGTTCGGATGTAGTACCTTCTGGTATGTGCACTTGTTCTACCAGAGCAGATTGGAGTGTAGGTGGAGAGGCTTGCACTGAGGGCGGAG[T/C]
CGGGGGAGCATGTTGTTTAGCTGGGGAGGTGGGAGAGGCTTAAACTGGTTGCGGAGCCGGGAGAGCAGGCTGTTGAGAAGGGGAGGGTGGTGGTGTAGGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.00%	0.90%	16.53%	41.58%	NA
All Indica	2759	8.00%	1.40%	24.72%	65.82%	NA
All Japonica	1512	98.30%	0.10%	0.13%	1.52%	NA
Aus	269	35.30%	0.00%	31.97%	32.71%	NA
Indica I	595	9.90%	0.30%	4.87%	84.87%	NA
Indica II	465	8.00%	3.00%	19.35%	69.68%	NA
Indica III	913	5.70%	0.00%	43.48%	50.82%	NA
Indica Intermediate	786	9.30%	3.10%	21.12%	66.54%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	97.60%	0.00%	0.20%	2.18%	NA
Japonica Intermediate	241	97.50%	0.40%	0.41%	1.66%	NA
VI/Aromatic	96	81.20%	0.00%	5.21%	13.54%	NA
Intermediate	90	63.30%	2.20%	6.67%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0212831375	A -> G	LOC_Os02g21610.1	upstream_gene_variant ; 3262.0bp to feature; MODIFIER	silent_mutation	Average:22.648; most accessible tissue: Callus, score: 47.132	N	N	N	N
vg0212831375	A -> G	LOC_Os02g21590.1	downstream_gene_variant ; 3689.0bp to feature; MODIFIER	silent_mutation	Average:22.648; most accessible tissue: Callus, score: 47.132	N	N	N	N
vg0212831375	A -> G	LOC_Os02g21600.1	intron_variant ; MODIFIER	silent_mutation	Average:22.648; most accessible tissue: Callus, score: 47.132	N	N	N	N
vg0212831375	A -> DEL	N	N	silent_mutation	Average:22.648; most accessible tissue: Callus, score: 47.132	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0212831375	NA	3.11E-09	mr1322	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
vg0212831375	NA	2.08E-14	mr1361	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
vg0212831375	NA	1.34E-11	mr1636	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
vg0212831375	NA	1.23E-06	mr1646	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
vg0212831375	NA	2.26E-07	mr1779	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
vg0212831375	2.53E-06	NA	mr1833	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
vg0212831375	4.41E-06	4.93E-06	mr1922	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