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Detailed information for vg0613478814:

Variant ID: vg0613478814 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13478814
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTATTACAACATTTTATTTAAATTTAATAAGTATTGAAAAATTACTTAGAATTCATAAAAACAATCCATAATATCTCTAGTACTTTTAATAAAAAAAGGT[G/A]
ACTATAAAACTTTCTATATTAATTAATTGGAAAAAAAGCTACATATTTAGTTGGCACTACGAGACCATAAGCAGTAGCCATGATATCAGGGCGTAGGTGC

Reverse complement sequence

GCACCTACGCCCTGATATCATGGCTACTGCTTATGGTCTCGTAGTGCCAACTAAATATGTAGCTTTTTTTCCAATTAATTAATATAGAAAGTTTTATAGT[C/T]
ACCTTTTTTTATTAAAAGTACTAGAGATATTATGGATTGTTTTTATGAATTCTAAGTAATTTTTCAATACTTATTAAATTTAAATAAAATGTTGTAATAG

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	90.60%	8.90%	0.51%	0.00%	NA
All Indica	2759	98.40%	1.50%	0.07%	0.00%	NA
All Japonica	1512	74.40%	24.40%	1.19%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	97.20%	2.80%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	96.70%	3.20%	0.13%	0.00%	NA
Temperate Japonica	767	96.20%	2.90%	0.91%	0.00%	NA
Tropical Japonica	504	39.90%	58.50%	1.59%	0.00%	NA
Japonica Intermediate	241	77.20%	21.60%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	10.00%	4.44%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0613478814	G -> A	LOC_Os06g23114.1	intron_variant ; MODIFIER	silent_mutation	Average:46.133; most accessible tissue: Minghui63 root, score: 65.279	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613478814	1.56E-08	NA	mr1033	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
vg0613478814	3.02E-07	8.33E-29	mr1301	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
vg0613478814	NA	5.89E-14	mr1301	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
vg0613478814	4.80E-06	3.22E-18	mr1410	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
vg0613478814	NA	2.69E-08	mr1593	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
vg0613478814	NA	9.21E-11	mr1993	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
vg0613478814	NA	8.86E-08	mr1993	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
vg0613478814	4.15E-13	NA	mr1033_2	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
vg0613478814	1.92E-06	5.96E-29	mr1301_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
vg0613478814	NA	3.61E-09	mr1354_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
vg0613478814	NA	3.83E-19	mr1410_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
vg0613478814	NA	2.52E-11	mr1593_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
vg0613478814	NA	7.63E-13	mr1993_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