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Detailed information for vg0618250316:

Variant ID: vg0618250316 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18250316
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGAGGTTCACTATCACCCCGGCAAGGCCAACGTTGTGGCCGACGCTTTGAGTCGGAAGAGCCATTGCAATCATCTGAGGACAGAAGGGATGGCTCCTGA[G/A]
CTTAAGGAGGAAATAGCCCAACTAAACCTACATATGGTACCTCATGGACAGATAAACACCTTGGACATTCAGCCTCTTCTGAGAACCCAAATAGAAGAAG

Reverse complement sequence

CTTCTTCTATTTGGGTTCTCAGAAGAGGCTGAATGTCCAAGGTGTTTATCTGTCCATGAGGTACCATATGTAGGTTTAGTTGGGCTATTTCCTCCTTAAG[C/T]
TCAGGAGCCATCCCTTCTGTCCTCAGATGATTGCAATGGCTCTTCCGACTCAAAGCGTCGGCCACAACGTTGGCCTTGCCGGGGTGATAGTGAACCTCTA

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	53.70%	4.30%	13.31%	28.61%	NA
All Indica	2759	29.30%	7.10%	18.16%	45.42%	NA
All Japonica	1512	98.30%	0.00%	0.13%	1.52%	NA
Aus	269	43.50%	1.10%	34.94%	20.45%	NA
Indica I	595	35.80%	8.70%	8.74%	46.72%	NA
Indica II	465	32.00%	4.30%	12.26%	51.40%	NA
Indica III	913	18.70%	8.80%	29.46%	43.04%	NA
Indica Intermediate	786	35.00%	5.70%	15.65%	43.64%	NA
Temperate Japonica	767	97.70%	0.00%	0.00%	2.35%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	97.90%	0.00%	0.83%	1.24%	NA
VI/Aromatic	96	56.20%	5.20%	31.25%	7.29%	NA
Intermediate	90	82.20%	0.00%	2.22%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618250316	G -> A	LOC_Os06g31350.1	synonymous_variant ; p.Glu927Glu; LOW	synonymous_codon	Average:11.795; most accessible tissue: Callus, score: 21.42	N	N	N	N
vg0618250316	G -> DEL	LOC_Os06g31350.1	N	frameshift_variant	Average:11.795; most accessible tissue: Callus, score: 21.42	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618250316	5.61E-06	8.54E-07	mr1547_2	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
vg0618250316	1.20E-06	1.41E-07	mr1547_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