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Detailed information for vg0606540226:

Variant ID: vg0606540226 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 6540226
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCATAATAGTGGAGGATGTCCTCATTATTTCCACCCCCTTAACAAGGGCCCAGCTCTGATACCAAATGGTAACGATCCGGCCCAGGTGGGGTTGGCCGAG[G/A]
CCCAATAACTTAAGGTTGCCTAGACCCCAACAGTTCATAGGCACACCCACTTGGGGAAAGGCCTAATCTCCCTAGAAAACTAGTCCGATAGGGGAAGGGT

Reverse complement sequence

ACCCTTCCCCTATCGGACTAGTTTTCTAGGGAGATTAGGCCTTTCCCCAAGTGGGTGTGCCTATGAACTGTTGGGGTCTAGGCAACCTTAAGTTATTGGG[C/T]
CTCGGCCAACCCCACCTGGGCCGGATCGTTACCATTTGGTATCAGAGCTGGGCCCTTGTTAAGGGGGTGGAAATAATGAGGACATCCTCCACTATTATGC

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	92.80%	4.80%	2.48%	0.00%	NA
All Indica	2759	99.50%	0.10%	0.47%	0.00%	NA
All Japonica	1512	78.40%	14.70%	6.88%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.00%	0.84%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.10%	0.76%	0.00%	NA
Temperate Japonica	767	63.10%	24.80%	12.13%	0.00%	NA
Tropical Japonica	504	98.60%	1.20%	0.20%	0.00%	NA
Japonica Intermediate	241	85.10%	10.80%	4.15%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0606540226	G -> A	LOC_Os06g12200.1	upstream_gene_variant ; 1549.0bp to feature; MODIFIER	silent_mutation	Average:55.547; most accessible tissue: Minghui63 young leaf, score: 78.821	N	N	N	N
vg0606540226	G -> A	LOC_Os06g12190.1	downstream_gene_variant ; 4329.0bp to feature; MODIFIER	silent_mutation	Average:55.547; most accessible tissue: Minghui63 young leaf, score: 78.821	N	N	N	N
vg0606540226	G -> A	LOC_Os06g12200-LOC_Os06g12210	intergenic_region ; MODIFIER	silent_mutation	Average:55.547; most accessible tissue: Minghui63 young leaf, score: 78.821	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0606540226	6.32E-06	NA	mr1300	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
vg0606540226	1.79E-06	NA	mr1309	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
vg0606540226	4.54E-07	4.53E-07	mr1609	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
vg0606540226	2.93E-06	NA	mr1841	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
vg0606540226	2.07E-06	NA	mr1900	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
vg0606540226	NA	9.95E-07	mr1900	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
vg0606540226	2.93E-07	NA	mr1926	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
vg0606540226	3.69E-07	NA	mr1238_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
vg0606540226	7.70E-06	NA	mr1310_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
vg0606540226	NA	5.20E-08	mr1364_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
vg0606540226	7.94E-07	NA	mr1484_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
vg0606540226	2.24E-06	NA	mr1609_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
vg0606540226	3.71E-07	3.71E-07	mr1609_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
vg0606540226	1.29E-07	NA	mr1841_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
vg0606540226	2.86E-07	NA	mr1900_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
vg0606540226	5.01E-07	NA	mr1945_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
vg0606540226	1.73E-06	NA	mr1959_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
vg0606540226	NA	8.10E-07	mr1959_2	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