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Detailed information for vg0619710671:

Variant ID: vg0619710671 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19710671
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTATAAATACACACACATACATGCATACCTATCCCTATAAATACACAACATACACCCCTACCCCTATGAAAATCTTCGAGAGATTGGACCGGCACATCTT[G/A]
ATATATTTTGAGATTAATTAAGTCACCATAAATATCTCTGTCAACGAGTAAACCTACCACTGATAAAATAATTAGCCGTAAAATACGAGATCACCCATGT

Reverse complement sequence

ACATGGGTGATCTCGTATTTTACGGCTAATTATTTTATCAGTGGTAGGTTTACTCGTTGACAGAGATATTTATGGTGACTTAATTAATCTCAAAATATAT[C/T]
AAGATGTGCCGGTCCAATCTCTCGAAGATTTTCATAGGGGTAGGGGTGTATGTTGTGTATTTATAGGGATAGGTATGCATGTATGTGTGTGTATTTATAG

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	64.70%	35.10%	0.15%	0.00%	NA
All Indica	2759	96.50%	3.30%	0.18%	0.00%	NA
All Japonica	1512	5.60%	94.40%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	97.50%	2.20%	0.34%	0.00%	NA
Indica II	465	95.90%	4.10%	0.00%	0.00%	NA
Indica III	913	98.80%	1.10%	0.11%	0.00%	NA
Indica Intermediate	786	93.40%	6.40%	0.25%	0.00%	NA
Temperate Japonica	767	3.40%	96.60%	0.00%	0.00%	NA
Tropical Japonica	504	10.70%	89.30%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	44.40%	53.30%	2.22%	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
vg0619710671	G -> A	LOC_Os06g33890.1	upstream_gene_variant ; 1826.0bp to feature; MODIFIER	silent_mutation	Average:52.655; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N
vg0619710671	G -> A	LOC_Os06g33880-LOC_Os06g33890	intergenic_region ; MODIFIER	silent_mutation	Average:52.655; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619710671	2.00E-13	1.58E-83	mr1033	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
vg0619710671	NA	1.65E-26	mr1072	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
vg0619710671	NA	6.51E-50	mr1154	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
vg0619710671	1.18E-10	2.64E-48	mr1176	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
vg0619710671	NA	2.11E-06	mr1278	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
vg0619710671	NA	2.30E-29	mr1333	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
vg0619710671	9.05E-06	8.22E-73	mr1536	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
vg0619710671	NA	1.86E-26	mr1686	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
vg0619710671	NA	2.15E-07	mr1824	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
vg0619710671	NA	1.95E-69	mr1865	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
vg0619710671	2.93E-16	1.39E-114	mr1033_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
vg0619710671	NA	6.92E-96	mr1536_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