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Detailed information for vg0113027848:

Variant ID: vg0113027848 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13027848
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAGGTTCTCCTCTGTTACATCGGAGGGCACCCACTGACTCTCGAAGCTTTCTCTCTCTTCTGCCATGAATACGAACTGGATGATGTGATTTGGTCCGAG[A/G]
TATGGCTGGGAATGGATGGGGGATCGATGCGGTGGTTGCACGGAAGGTTTTTGTGGAGCTCAAGAGGATGGATCGGAGTGGATTTGTTAACCCTAGCTTT

Reverse complement sequence

AAAGCTAGGGTTAACAAATCCACTCCGATCCATCCTCTTGAGCTCCACAAAAACCTTCCGTGCAACCACCGCATCGATCCCCCATCCATTCCCAGCCATA[T/C]
CTCGGACCAAATCACATCATCCAGTTCGTATTCATGGCAGAAGAGAGAGAAAGCTTCGAGAGTCAGTGGGTGCCCTCCGATGTAACAGAGGAGAACCTGA

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	53.60%	0.40%	4.23%	41.75%	NA
All Indica	2759	30.10%	0.80%	5.04%	64.12%	NA
All Japonica	1512	98.20%	0.00%	0.20%	1.59%	NA
Aus	269	29.00%	0.00%	16.73%	54.28%	NA
Indica I	595	51.90%	0.70%	3.03%	44.37%	NA
Indica II	465	37.60%	1.10%	5.38%	55.91%	NA
Indica III	913	7.60%	0.50%	5.15%	86.75%	NA
Indica Intermediate	786	35.20%	0.90%	6.23%	57.63%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	95.60%	0.00%	0.00%	4.37%	NA
Japonica Intermediate	241	98.80%	0.00%	0.83%	0.41%	NA
VI/Aromatic	96	70.80%	0.00%	9.38%	19.79%	NA
Intermediate	90	78.90%	0.00%	4.44%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113027848	A -> G	LOC_Os01g23190.1	upstream_gene_variant ; 4603.0bp to feature; MODIFIER	silent_mutation	Average:9.362; most accessible tissue: Callus, score: 17.544	N	N	N	N
vg0113027848	A -> G	LOC_Os01g23180.1	intron_variant ; MODIFIER	silent_mutation	Average:9.362; most accessible tissue: Callus, score: 17.544	N	N	N	N
vg0113027848	A -> DEL	N	N	silent_mutation	Average:9.362; most accessible tissue: Callus, score: 17.544	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113027848	NA	1.47E-06	mr1285	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
vg0113027848	1.11E-06	1.16E-07	mr1656	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
vg0113027848	2.85E-06	2.85E-06	mr1656	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