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Detailed information for vg0621412586:

Variant ID: vg0621412586 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 21412586
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCCGTCCCGTCAGGAGGATGTTCGGAGGACAACCGTGCAAATCTCCGTCCATTTATGAAGAGAAGAAAAGTCCAGTTTGGAAAGAGAGGGGTGCATGTG[G/C]
TATCCCCTTGAAGTATAAAAGGAGGACCCTGCCCATGGGGAAGGGGGATGATCTTTTCCAGATTCAGTAGCTAGAAGAAAAGGGGGAGGTTGGCTCACAC

Reverse complement sequence

GTGTGAGCCAACCTCCCCCTTTTCTTCTAGCTACTGAATCTGGAAAAGATCATCCCCCTTCCCCATGGGCAGGGTCCTCCTTTTATACTTCAAGGGGATA[C/G]
CACATGCACCCCTCTCTTTCCAAACTGGACTTTTCTTCTCTTCATAAATGGACGGAGATTTGCACGGTTGTCCTCCGAACATCCTCCTGACGGGACGGCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.10%	0.30%	5.18%	11.43%	NA
All Indica	2759	84.30%	0.50%	8.05%	7.18%	NA
All Japonica	1512	89.40%	0.00%	0.66%	9.99%	NA
Aus	269	27.90%	0.00%	2.97%	69.14%	NA
Indica I	595	80.20%	0.80%	13.78%	5.21%	NA
Indica II	465	84.70%	0.40%	6.88%	7.96%	NA
Indica III	913	87.60%	0.20%	3.83%	8.32%	NA
Indica Intermediate	786	83.20%	0.60%	9.29%	6.87%	NA
Temperate Japonica	767	81.70%	0.00%	0.78%	17.47%	NA
Tropical Japonica	504	98.40%	0.00%	0.79%	0.79%	NA
Japonica Intermediate	241	94.60%	0.00%	0.00%	5.39%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	91.10%	0.00%	3.33%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0621412586	G -> C	LOC_Os06g36470.1	downstream_gene_variant ; 2263.0bp to feature; MODIFIER	silent_mutation	Average:26.751; most accessible tissue: Minghui63 root, score: 45.031	N	N	N	N
vg0621412586	G -> C	LOC_Os06g36480.1	downstream_gene_variant ; 1588.0bp to feature; MODIFIER	silent_mutation	Average:26.751; most accessible tissue: Minghui63 root, score: 45.031	N	N	N	N
vg0621412586	G -> C	LOC_Os06g36470-LOC_Os06g36480	intergenic_region ; MODIFIER	silent_mutation	Average:26.751; most accessible tissue: Minghui63 root, score: 45.031	N	N	N	N
vg0621412586	G -> DEL	N	N	silent_mutation	Average:26.751; most accessible tissue: Minghui63 root, score: 45.031	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0621412586	3.09E-06	NA	mr1184_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
vg0621412586	5.26E-06	3.67E-06	mr1184_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
vg0621412586	NA	2.85E-08	mr1212_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
vg0621412586	8.83E-06	NA	mr1284_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
vg0621412586	5.50E-06	NA	mr1374_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
vg0621412586	3.12E-06	3.12E-06	mr1374_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
vg0621412586	5.05E-06	5.04E-06	mr1412_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
vg0621412586	7.25E-06	7.25E-06	mr1412_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
vg0621412586	NA	9.89E-06	mr1417_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
vg0621412586	3.34E-06	3.34E-06	mr1440_2	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
vg0621412586	NA	9.54E-06	mr1641_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
vg0621412586	6.44E-06	3.93E-06	mr1683_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
vg0621412586	8.06E-06	1.32E-06	mr1747_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
vg0621412586	2.41E-06	2.41E-06	mr1747_2	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
vg0621412586	3.30E-06	NA	mr1811_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
vg0621412586	7.50E-06	4.36E-06	mr1811_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
vg0621412586	2.45E-06	5.91E-06	mr1816_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
vg0621412586	4.26E-06	4.26E-06	mr1816_2	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
vg0621412586	NA	2.65E-06	mr1831_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
vg0621412586	3.52E-06	3.92E-06	mr1831_2	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
vg0621412586	NA	3.50E-06	mr1840_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
vg0621412586	NA	4.69E-06	mr1856_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