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Detailed information for vg1217854401:

Variant ID: vg1217854401 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17854401
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAATTAAGCTTTGCAACTATAAAACATGTGTAAGCGCTAGCCTGGAAAAGACAGGAAGGCTACGCTGTTGACATGCGGACCCCACATGTCAACCTAAGG[G/A]
ACCACGGTAGACCGAGTACACAGAGACGGTCCACGGGTCGACGGAAGCGGACCCCGTGTGTCAACCGAGGCGAGTGGTTGTCAAACGGACTCCACTAGAC

Reverse complement sequence

GTCTAGTGGAGTCCGTTTGACAACCACTCGCCTCGGTTGACACACGGGGTCCGCTTCCGTCGACCCGTGGACCGTCTCTGTGTACTCGGTCTACCGTGGT[C/T]
CCTTAGGTTGACATGTGGGGTCCGCATGTCAACAGCGTAGCCTTCCTGTCTTTTCCAGGCTAGCGCTTACACATGTTTTATAGTTGCAAAGCTTAATTAT

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	63.50%	1.60%	3.30%	31.65%	NA
All Indica	2759	54.40%	2.60%	4.17%	38.75%	NA
All Japonica	1512	79.80%	0.10%	1.39%	18.72%	NA
Aus	269	55.40%	0.00%	4.83%	39.78%	NA
Indica I	595	59.50%	1.00%	3.53%	35.97%	NA
Indica II	465	55.90%	0.20%	3.44%	40.43%	NA
Indica III	913	47.20%	2.80%	4.93%	45.02%	NA
Indica Intermediate	786	58.10%	5.10%	4.20%	32.57%	NA
Temperate Japonica	767	97.90%	0.00%	0.13%	1.96%	NA
Tropical Japonica	504	58.10%	0.00%	2.58%	39.29%	NA
Japonica Intermediate	241	67.20%	0.80%	2.90%	29.05%	NA
VI/Aromatic	96	74.00%	0.00%	5.21%	20.83%	NA
Intermediate	90	78.90%	0.00%	2.22%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217854401	G -> DEL	N	N	silent_mutation	Average:8.15; most accessible tissue: Minghui63 young leaf, score: 11.521	N	N	N	N
vg1217854401	G -> A	LOC_Os12g29860.1	upstream_gene_variant ; 531.0bp to feature; MODIFIER	silent_mutation	Average:8.15; most accessible tissue: Minghui63 young leaf, score: 11.521	N	N	N	N
vg1217854401	G -> A	LOC_Os12g29850.1	downstream_gene_variant ; 2027.0bp to feature; MODIFIER	silent_mutation	Average:8.15; most accessible tissue: Minghui63 young leaf, score: 11.521	N	N	N	N
vg1217854401	G -> A	LOC_Os12g29850-LOC_Os12g29860	intergenic_region ; MODIFIER	silent_mutation	Average:8.15; most accessible tissue: Minghui63 young leaf, score: 11.521	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217854401	2.46E-07	2.45E-09	mr1768_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