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Detailed information for vg0117203916:

Variant ID: vg0117203916 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 17203916
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCTTGAAGAGAGAACGGAAACAATTTCCACGGCACAGTTTCTTGTCTCATGCCACAAAGAAAATGATGGTAGGGATTTTCTAGATCAAACCAAGAAAA[A/G]
GGATTTTCCCTAACCATATTGATTAGTTCGGGGCGAATTTCATAGACAGTTGTATAAATGGGCTCCGATGAAGGAGGTGGCTCATAGAATTCGCCCCGAG

Reverse complement sequence

CTCGGGGCGAATTCTATGAGCCACCTCCTTCATCGGAGCCCATTTATACAACTGTCTATGAAATTCGCCCCGAACTAATCAATATGGTTAGGGAAAATCC[T/C]
TTTTCTTGGTTTGATCTAGAAAATCCCTACCATCATTTTCTTTGTGGCATGAGACAAGAAACTGTGCCGTGGAAATTGTTTCCGTTCTCTCTTCAAGAAA

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	96.40%	2.20%	1.08%	0.25%	NA
All Indica	2759	94.90%	3.10%	1.70%	0.36%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	92.60%	7.10%	0.37%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	83.20%	10.80%	4.95%	1.08%	NA
Indica III	913	97.20%	0.90%	1.53%	0.44%	NA
Indica Intermediate	786	95.40%	3.40%	1.02%	0.13%	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	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	93.30%	2.20%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0117203916	A -> G	LOC_Os01g31460.1	upstream_gene_variant ; 463.0bp to feature; MODIFIER	silent_mutation	Average:30.474; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0117203916	A -> G	LOC_Os01g31460-LOC_Os01g31470	intergenic_region ; MODIFIER	silent_mutation	Average:30.474; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0117203916	A -> DEL	N	N	silent_mutation	Average:30.474; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0117203916	4.03E-06	1.16E-06	mr1043	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
vg0117203916	2.05E-06	NA	mr1043	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