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Detailed information for vg0517105581:

Variant ID: vg0517105581 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17105581
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCAAGGAAATGGTACAGTTTACACGATTGATTCCTGTTTAAAAACAAGGGTCCATAGAGCTGGTATCAGAGCCATACAACTGTAGGAAAAGACCAAAAG[G/A]
CGCCTCACCCCTTTTCTAGTTGGTCAAGGGAGAAATTCCCATTTAGTAATACTTTCAAAAATAGAAAAAACGCTATGTTTACAAAACTCTATACGATTTT

Reverse complement sequence

AAAATCGTATAGAGTTTTGTAAACATAGCGTTTTTTCTATTTTTGAAAGTATTACTAAATGGGAATTTCTCCCTTGACCAACTAGAAAAGGGGTGAGGCG[C/T]
CTTTTGGTCTTTTCCTACAGTTGTATGGCTCTGATACCAGCTCTATGGACCCTTGTTTTTAAACAGGAATCAATCGTGTAAACTGTACCATTTCCTTGGA

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	96.70%	3.10%	0.25%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	90.50%	8.80%	0.73%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	72.60%	25.60%	1.79%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0517105581	G -> A	LOC_Os05g29120.1	upstream_gene_variant ; 409.0bp to feature; MODIFIER	silent_mutation	Average:43.24; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0517105581	G -> A	LOC_Os05g29110-LOC_Os05g29120	intergenic_region ; MODIFIER	silent_mutation	Average:43.24; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517105581	3.99E-06	3.25E-07	mr1218_2	Jap_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