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Detailed information for vg1213045482:

Variant ID: vg1213045482 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13045482
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCGGCCCTACCTCAACGGCTGTCCTACCGTAGCACACCTGCCTCACTCAGGGGTGAACCATCTATGCAGGGATACTGCCTCTGCTCGGCTATCTACTCC[A/G]
CTAGGTCTATACCCATACGAGAAGTGCGGTTGTACGAGGGTCGTTTCATGCTTAACTTCATGGCTCGGTCCTTAATTGACCGGGGAAGGTACTAGCCTTT

Reverse complement sequence

AAAGGCTAGTACCTTCCCCGGTCAATTAAGGACCGAGCCATGAAGTTAAGCATGAAACGACCCTCGTACAACCGCACTTCTCGTATGGGTATAGACCTAG[T/C]
GGAGTAGATAGCCGAGCAGAGGCAGTATCCCTGCATAGATGGTTCACCCCTGAGTGAGGCAGGTGTGCTACGGTAGGACAGCCGTTGAGGTAGGGCCGAG

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	17.00%	0.50%	58.59%	23.89%	NA
All Indica	2759	4.30%	0.70%	83.15%	11.89%	NA
All Japonica	1512	43.60%	0.30%	8.40%	47.75%	NA
Aus	269	0.40%	0.40%	86.62%	12.64%	NA
Indica I	595	2.00%	0.30%	73.61%	24.03%	NA
Indica II	465	4.90%	1.70%	76.77%	16.56%	NA
Indica III	913	3.50%	0.50%	92.77%	3.18%	NA
Indica Intermediate	786	6.50%	0.50%	82.95%	10.05%	NA
Temperate Japonica	767	78.00%	0.30%	5.74%	16.04%	NA
Tropical Japonica	504	1.00%	0.40%	7.34%	91.27%	NA
Japonica Intermediate	241	23.20%	0.00%	19.09%	57.68%	NA
VI/Aromatic	96	1.00%	0.00%	77.08%	21.88%	NA
Intermediate	90	27.80%	0.00%	45.56%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213045482	A -> DEL	N	N	silent_mutation	Average:8.256; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1213045482	A -> G	LOC_Os12g23080.1	upstream_gene_variant ; 2545.0bp to feature; MODIFIER	silent_mutation	Average:8.256; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1213045482	A -> G	LOC_Os12g23080-LOC_Os12g23090	intergenic_region ; MODIFIER	silent_mutation	Average:8.256; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213045482	NA	8.22E-08	mr1639	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