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Detailed information for vg0413759612:

Variant ID: vg0413759612 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13759612
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGCAGGGGATGGGTGGGGAAGGGGAGGAGGCGGAGGGGGAGGAGGAGAGAGATCGATCTGAGAGGAGGAGGGGAGGAGGAGAGGGAGATCGATCTGAGC[C/G]
GATGGGAAGGGAGTACGGGGAGGAGAGGGCCGGGGATGGGAGGAGGAAGGGGAGAAGGCGGAGGCGGAGGAGGAGAGGGAGATCGATCTGAGAGGGAGGA

Reverse complement sequence

TCCTCCCTCTCAGATCGATCTCCCTCTCCTCCTCCGCCTCCGCCTTCTCCCCTTCCTCCTCCCATCCCCGGCCCTCTCCTCCCCGTACTCCCTTCCCATC[G/C]
GCTCAGATCGATCTCCCTCTCCTCCTCCCCTCCTCCTCTCAGATCGATCTCTCTCCTCCTCCCCCTCCGCCTCCTCCCCTTCCCCACCCATCCCCTGCCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.80%	3.80%	9.84%	7.49%	NA
All Indica	2759	75.90%	4.00%	11.49%	8.59%	NA
All Japonica	1512	91.30%	2.80%	4.56%	1.32%	NA
Aus	269	56.10%	0.40%	11.90%	31.60%	NA
Indica I	595	77.00%	3.00%	12.94%	7.06%	NA
Indica II	465	60.00%	14.80%	16.77%	8.39%	NA
Indica III	913	82.40%	0.40%	7.45%	9.75%	NA
Indica Intermediate	786	77.00%	2.50%	11.96%	8.52%	NA
Temperate Japonica	767	98.30%	0.30%	1.30%	0.13%	NA
Tropical Japonica	504	86.70%	4.40%	6.94%	1.98%	NA
Japonica Intermediate	241	78.40%	7.90%	9.96%	3.73%	NA
VI/Aromatic	96	42.70%	19.80%	31.25%	6.25%	NA
Intermediate	90	66.70%	7.80%	18.89%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0413759612	C -> DEL	N	N	silent_mutation	Average:56.874; most accessible tissue: Zhenshan97 flag leaf, score: 75.455	N	N	N	N
vg0413759612	C -> G	LOC_Os04g24090.1	downstream_gene_variant ; 994.0bp to feature; MODIFIER	silent_mutation	Average:56.874; most accessible tissue: Zhenshan97 flag leaf, score: 75.455	N	N	N	N
vg0413759612	C -> G	LOC_Os04g24100.1	downstream_gene_variant ; 2944.0bp to feature; MODIFIER	silent_mutation	Average:56.874; most accessible tissue: Zhenshan97 flag leaf, score: 75.455	N	N	N	N
vg0413759612	C -> G	LOC_Os04g24080-LOC_Os04g24090	intergenic_region ; MODIFIER	silent_mutation	Average:56.874; most accessible tissue: Zhenshan97 flag leaf, score: 75.455	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413759612	6.23E-08	NA	mr1584	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
vg0413759612	1.81E-06	NA	mr1730	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
vg0413759612	2.76E-06	NA	mr1866	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
vg0413759612	1.93E-09	NA	mr1350_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
vg0413759612	3.22E-08	3.69E-11	mr1350_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
vg0413759612	2.15E-06	NA	mr1368_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
vg0413759612	1.24E-14	NA	mr1730_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
vg0413759612	1.30E-09	1.30E-09	mr1730_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
vg0413759612	1.59E-07	1.92E-08	mr1730_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
vg0413759612	5.23E-06	NA	mr1853_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
vg0413759612	1.43E-11	NA	mr1866_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
vg0413759612	4.66E-07	3.03E-06	mr1866_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