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Detailed information for vg1215225558:

Variant ID: vg1215225558 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15225558
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCTACATGTTTGGTTAAGGTAAATGAAAAATTTGAATTAAAGAATGTAGCTTTGGTTAAGGACTTAAAGTACAATTTGCTTTCGGTTTCACAAATTGTT[G/A]
ATGAAGAATTTGAAGTTCACTTTAAGAAAACTGGAAGTAAAGTTTTTGATTCTCGTGGTGATTCTGTGCTGAATATTTCTCGCTATGGAAGAGTGTTTAA

Reverse complement sequence

TTAAACACTCTTCCATAGCGAGAAATATTCAGCACAGAATCACCACGAGAATCAAAAACTTTACTTCCAGTTTTCTTAAAGTGAACTTCAAATTCTTCAT[C/T]
AACAATTTGTGAAACCGAAAGCAAATTGTACTTTAAGTCCTTAACCAAAGCTACATTCTTTAATTCAAATTTTTCATTTACCTTAACCAAACATGTAGCG

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	87.70%	0.70%	7.96%	3.66%	NA
All Indica	2759	89.50%	0.10%	5.94%	4.53%	NA
All Japonica	1512	88.50%	1.90%	7.08%	2.58%	NA
Aus	269	66.20%	0.00%	32.34%	1.49%	NA
Indica I	595	89.20%	0.00%	4.20%	6.55%	NA
Indica II	465	95.70%	0.40%	1.51%	2.37%	NA
Indica III	913	86.90%	0.00%	8.76%	4.38%	NA
Indica Intermediate	786	88.90%	0.00%	6.62%	4.45%	NA
Temperate Japonica	767	98.70%	0.00%	0.78%	0.52%	NA
Tropical Japonica	504	74.60%	4.40%	16.27%	4.76%	NA
Japonica Intermediate	241	85.10%	2.50%	7.88%	4.56%	NA
VI/Aromatic	96	85.40%	2.10%	10.42%	2.08%	NA
Intermediate	90	87.80%	0.00%	8.89%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215225558	G -> DEL	LOC_Os12g26140.1	N	frameshift_variant	Average:8.095; most accessible tissue: Callus, score: 24.058	N	N	N	N
vg1215225558	G -> A	LOC_Os12g26140.1	missense_variant ; p.Asp585Asn; MODERATE	nonsynonymous_codon ; D585N	Average:8.095; most accessible tissue: Callus, score: 24.058	unknown	unknown	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215225558	7.68E-06	7.68E-06	mr1427_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