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Detailed information for vg0405832147:

Variant ID: vg0405832147 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5832147
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCCGACTAGTCATAGCCCCCAAGCACCAGGAGTCGGCCTAGGCACTTCCCAAACATGCATACGAGTGATATGAGTTCGTCATTAATGGAACAAAGTTTC[A/G]
CGGGTCAGAGTTTACTACTTGGGTACTTTTGCAATTATTAAGAGCAGAAAACAAATTTATTTTATCTCTATGCTTTTGATTTATTCTGAATAATACTTAG

Reverse complement sequence

CTAAGTATTATTCAGAATAAATCAAAAGCATAGAGATAAAATAAATTTGTTTTCTGCTCTTAATAATTGCAAAAGTACCCAAGTAGTAAACTCTGACCCG[T/C]
GAAACTTTGTTCCATTAATGACGAACTCATATCACTCGTATGCATGTTTGGGAAGTGCCTAGGCCGACTCCTGGTGCTTGGGGGCTATGACTAGTCGGGC

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	33.70%	6.10%	4.97%	55.21%	NA
All Indica	2759	7.90%	6.40%	5.51%	80.21%	NA
All Japonica	1512	80.40%	0.10%	0.20%	19.31%	NA
Aus	269	9.70%	40.50%	26.02%	23.79%	NA
Indica I	595	2.90%	2.90%	1.51%	92.77%	NA
Indica II	465	11.00%	1.70%	6.88%	80.43%	NA
Indica III	913	9.00%	13.50%	7.45%	70.10%	NA
Indica Intermediate	786	8.50%	3.70%	5.47%	82.32%	NA
Temperate Japonica	767	94.30%	0.10%	0.13%	5.48%	NA
Tropical Japonica	504	56.50%	0.00%	0.20%	43.25%	NA
Japonica Intermediate	241	85.90%	0.40%	0.41%	13.28%	NA
VI/Aromatic	96	95.80%	1.00%	2.08%	1.04%	NA
Intermediate	90	46.70%	1.10%	8.89%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405832147	A -> DEL	N	N	silent_mutation	Average:8.559; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg0405832147	A -> G	LOC_Os04g10720.1	upstream_gene_variant ; 4492.0bp to feature; MODIFIER	silent_mutation	Average:8.559; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg0405832147	A -> G	LOC_Os04g10724.1	downstream_gene_variant ; 2434.0bp to feature; MODIFIER	silent_mutation	Average:8.559; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg0405832147	A -> G	LOC_Os04g10740.1	downstream_gene_variant ; 3011.0bp to feature; MODIFIER	silent_mutation	Average:8.559; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N
vg0405832147	A -> G	LOC_Os04g10730.1	intron_variant ; MODIFIER	silent_mutation	Average:8.559; most accessible tissue: Minghui63 root, score: 13.235	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405832147	NA	2.89E-06	mr1054	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
vg0405832147	NA	2.46E-07	mr1073	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
vg0405832147	NA	3.59E-07	mr1209	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
vg0405832147	NA	7.45E-11	mr1232	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
vg0405832147	NA	1.81E-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
vg0405832147	NA	5.33E-06	mr1287	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
vg0405832147	NA	7.80E-06	mr1293	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
vg0405832147	NA	2.33E-07	mr1297	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
vg0405832147	1.73E-06	9.08E-08	mr1312	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
vg0405832147	NA	3.10E-06	mr1345	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
vg0405832147	NA	5.94E-06	mr1372	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
vg0405832147	NA	3.99E-06	mr1382	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
vg0405832147	NA	1.78E-06	mr1433	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
vg0405832147	NA	2.04E-07	mr1434	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
vg0405832147	NA	1.44E-06	mr1512	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
vg0405832147	NA	3.32E-07	mr1633	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
vg0405832147	NA	7.96E-12	mr1649	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
vg0405832147	NA	1.63E-06	mr1665	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
vg0405832147	NA	1.93E-07	mr1687	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
vg0405832147	NA	3.22E-08	mr1777	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
vg0405832147	NA	1.02E-07	mr1787	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
vg0405832147	NA	3.79E-10	mr1939	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
vg0405832147	6.78E-07	1.42E-09	mr1963	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
vg0405832147	NA	9.14E-06	mr1963	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