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Detailed information for vg0220988854:

Variant ID: vg0220988854 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20988854
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACAATAACCCACTCGTGCCGGCTTGTGTTGCGTCGTCTGTCCGCCCCTCTTGGTTCCTAACAGCAAGTCCAGGCATCGCCTCACTCCAGGTGGCTGGCC[G/A]
AGCAAGTATGCTCAGTTCATAGATTTTGGTATTCAGGTGTATATGTTCTGCAATAGAAAGTTTACAAAGAATGCAAAATTACGAAGGGTAGGACGCAAAC

Reverse complement sequence

GTTTGCGTCCTACCCTTCGTAATTTTGCATTCTTTGTAAACTTTCTATTGCAGAACATATACACCTGAATACCAAAATCTATGAACTGAGCATACTTGCT[C/T]
GGCCAGCCACCTGGAGTGAGGCGATGCCTGGACTTGCTGTTAGGAACCAAGAGGGGCGGACAGACGACGCAACACAAGCCGGCACGAGTGGGTTATTGTT

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	79.50%	12.50%	8.04%	0.00%	NA
All Indica	2759	67.10%	19.60%	13.34%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	82.90%	13.40%	3.72%	0.00%	NA
Indica I	595	81.80%	12.60%	5.55%	0.00%	NA
Indica II	465	67.10%	20.40%	12.47%	0.00%	NA
Indica III	913	54.70%	24.80%	20.59%	0.00%	NA
Indica Intermediate	786	70.40%	18.30%	11.32%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	6.70%	2.22%	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
vg0220988854	G -> A	LOC_Os02g34990.1	upstream_gene_variant ; 819.0bp to feature; MODIFIER	silent_mutation	Average:29.933; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0220988854	G -> A	LOC_Os02g34990.2	intron_variant ; MODIFIER	silent_mutation	Average:29.933; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220988854	6.46E-06	NA	mr1084	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
vg0220988854	2.07E-07	1.24E-07	mr1084	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
vg0220988854	NA	2.57E-06	mr1106	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
vg0220988854	NA	3.83E-06	mr1347	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
vg0220988854	NA	1.50E-07	mr1347	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
vg0220988854	NA	3.47E-06	mr1441	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
vg0220988854	9.21E-06	9.21E-06	mr1492	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
vg0220988854	9.01E-06	6.75E-07	mr1641	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
vg0220988854	NA	6.75E-06	mr1839	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
vg0220988854	2.54E-06	2.53E-06	mr1869	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
vg0220988854	1.25E-06	1.25E-06	mr1869	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