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Detailed information for vg1023023087:

Variant ID: vg1023023087 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 23023087
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACTCATTCATACTTTAAATGTTGTATGGGTTGAACAAATAGAAATTAATCTTGATTTGCTGCATGAATGAGGCATGTTTATTTGGGGAATTTTTTTTTG[G/A]
TTTTGGTTATCACATTGGATATATGGACACACATTTGAAGTATTAAATGTAGTCTAATAACAAAACAAATTATAGTTTCCACTAGAAAACCGTGAGATGA

Reverse complement sequence

TCATCTCACGGTTTTCTAGTGGAAACTATAATTTGTTTTGTTATTAGACTACATTTAATACTTCAAATGTGTGTCCATATATCCAATGTGATAACCAAAA[C/T]
CAAAAAAAAATTCCCCAAATAAACATGCCTCATTCATGCAGCAAATCAAGATTAATTTCTATTTGTTCAACCCATACAACATTTAAAGTATGAATGAGTT

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	97.40%	2.00%	0.66%	0.00%	NA
All Indica	2759	95.50%	3.40%	1.12%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.60%	4.50%	2.86%	0.00%	NA
Indica II	465	98.90%	0.20%	0.86%	0.00%	NA
Indica III	913	94.60%	5.10%	0.22%	0.00%	NA
Indica Intermediate	786	96.70%	2.30%	1.02%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1023023087	G -> A	LOC_Os10g42690.1	upstream_gene_variant ; 2627.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1023023087	G -> A	LOC_Os10g42670-LOC_Os10g42690	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1023023087	2.05E-06	3.33E-07	mr1454_2	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
vg1023023087	NA	9.11E-06	mr1636_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