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Detailed information for vg0610633502:

Variant ID: vg0610633502 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10633502
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCCTTTGACGATTAGTCGCTTGGCGCCAAGTGCGGCTGCATCTCGTATCCCGGCAAGTAGTCCTTCGTATTCTGCAGTGTTATTCGTTGCTCTGAAGTT[A/G]
AGGTGGATTGCGTGTTTGAATTGATCTCCGGATGGAGATGTTAAGATAAATCCAGCGCCTGCTCCTTGGCTATTGAGTGCACCATCGAACGCCATTGTCC

Reverse complement sequence

GGACAATGGCGTTCGATGGTGCACTCAATAGCCAAGGAGCAGGCGCTGGATTTATCTTAACATCTCCATCCGGAGATCAATTCAAACACGCAATCCACCT[T/C]
AACTTCAGAGCAACGAATAACACTGCAGAATACGAAGGACTACTTGCCGGGATACGAGATGCAGCCGCACTTGGCGCCAAGCGACTAATCGTCAAAGGGG

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	58.00%	1.80%	25.92%	14.28%	NA
All Indica	2759	65.50%	2.50%	30.23%	1.78%	NA
All Japonica	1512	49.70%	0.30%	9.79%	40.21%	NA
Aus	269	17.50%	4.50%	77.32%	0.74%	NA
Indica I	595	75.30%	2.70%	20.67%	1.34%	NA
Indica II	465	65.60%	3.70%	30.54%	0.22%	NA
Indica III	913	55.30%	1.40%	39.87%	3.40%	NA
Indica Intermediate	786	69.80%	2.90%	26.08%	1.15%	NA
Temperate Japonica	767	48.80%	0.10%	3.91%	47.20%	NA
Tropical Japonica	504	54.80%	0.60%	17.46%	27.18%	NA
Japonica Intermediate	241	42.30%	0.00%	12.45%	45.23%	NA
VI/Aromatic	96	75.00%	0.00%	17.71%	7.29%	NA
Intermediate	90	68.90%	1.10%	20.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610633502	A -> G	LOC_Os06g18750.1	downstream_gene_variant ; 2280.0bp to feature; MODIFIER	silent_mutation	Average:20.399; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0610633502	A -> G	LOC_Os06g18750-LOC_Os06g18770	intergenic_region ; MODIFIER	silent_mutation	Average:20.399; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0610633502	A -> DEL	N	N	silent_mutation	Average:20.399; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610633502	1.88E-11	NA	mr1087	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
vg0610633502	1.70E-07	5.84E-10	mr1087	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
vg0610633502	NA	2.19E-07	mr1087	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
vg0610633502	2.25E-07	NA	mr1096	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
vg0610633502	2.32E-06	NA	mr1110	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
vg0610633502	1.65E-06	NA	mr1112	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
vg0610633502	NA	3.19E-06	mr1844	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
vg0610633502	8.07E-06	1.17E-07	mr1078_2	Ind_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
vg0610633502	2.47E-10	NA	mr1087_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
vg0610633502	5.50E-06	1.05E-10	mr1087_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
vg0610633502	NA	9.91E-07	mr1090_2	Ind_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
vg0610633502	NA	4.38E-06	mr1096_2	Ind_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