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Detailed information for vg0615550236:

Variant ID: vg0615550236 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 15550236
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAACTGCTTCTAGGCCAGACATACAATTTGCTGTGTGTTTGTGTGCGCGCTTTCAAGCTTCTCCTCGTGCTTCACATCGTTAAGCGGTCAAGCGAATAAT[A/G]
AGGTATTTGAATCATACACTTGAGTTTGGAATTTTGTATTCTACTTCATCTTCTATATGCTTAAGTGGATATTCCGATGCTGATTTTGGAGGTTGTAGAA

Reverse complement sequence

TTCTACAACCTCCAAAATCAGCATCGGAATATCCACTTAAGCATATAGAAGATGAAGTAGAATACAAAATTCCAAACTCAAGTGTATGATTCAAATACCT[T/C]
ATTATTCGCTTGACCGCTTAACGATGTGAAGCACGAGGAGAAGCTTGAAAGCGCGCACACAAACACACAGCAAATTGTATGTCTGGCCTAGAAGCAGTTA

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	32.10%	0.10%	7.55%	60.20%	NA
All Indica	2759	3.70%	0.10%	0.87%	95.32%	NA
All Japonica	1512	91.00%	0.10%	5.82%	3.04%	NA
Aus	269	1.50%	0.40%	57.62%	40.52%	NA
Indica I	595	5.00%	0.00%	0.34%	94.62%	NA
Indica II	465	2.20%	0.20%	0.86%	96.77%	NA
Indica III	913	2.40%	0.10%	1.10%	96.39%	NA
Indica Intermediate	786	5.20%	0.00%	1.02%	93.77%	NA
Temperate Japonica	767	96.30%	0.00%	0.26%	3.39%	NA
Tropical Japonica	504	82.30%	0.20%	14.48%	2.98%	NA
Japonica Intermediate	241	92.10%	0.40%	5.39%	2.07%	NA
VI/Aromatic	96	2.10%	0.00%	83.33%	14.58%	NA
Intermediate	90	37.80%	0.00%	11.11%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0615550236	A -> G	LOC_Os06g27450.1	upstream_gene_variant ; 4584.0bp to feature; MODIFIER	silent_mutation	Average:14.162; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N
vg0615550236	A -> G	LOC_Os06g27470.1	downstream_gene_variant ; 2932.0bp to feature; MODIFIER	silent_mutation	Average:14.162; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N
vg0615550236	A -> G	LOC_Os06g27460.1	intron_variant ; MODIFIER	silent_mutation	Average:14.162; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N
vg0615550236	A -> DEL	N	N	silent_mutation	Average:14.162; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0615550236	1.89E-06	NA	mr1158	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
vg0615550236	3.53E-07	3.53E-07	mr1536	Jap_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
vg0615550236	NA	1.95E-10	mr1581	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