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Detailed information for vg0619747679:

Variant ID: vg0619747679 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19747679
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTATATATGATTCTGAAAATCACTTTCATTGAGATATACTCCCTCCGTTTCAAAATGTTTGACACCGTTGACTTTTTAAGTACGTGTTTGACCATTCGT[T/C]
TTATTCAAAAAATTTAAGTAATTATTTATTCTTTTCATATCATTTGATTCATCGTTAAATATACTTTCATGTACACATATAGTTTTACATATTTCACAAA

Reverse complement sequence

TTTGTGAAATATGTAAAACTATATGTGTACATGAAAGTATATTTAACGATGAATCAAATGATATGAAAAGAATAAATAATTACTTAAATTTTTTGAATAA[A/G]
ACGAATGGTCAAACACGTACTTAAAAAGTCAACGGTGTCAAACATTTTGAAACGGAGGGAGTATATCTCAATGAAAGTGATTTTCAGAATCATATATAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.90%	8.00%	0.11%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	83.80%	15.90%	0.33%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	97.30%	2.70%	0.00%	0.00%	NA
Temperate Japonica	767	73.50%	25.90%	0.52%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	83.80%	15.80%	0.41%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0619747679	T -> C	LOC_Os06g33940.1	upstream_gene_variant ; 1222.0bp to feature; MODIFIER	silent_mutation	Average:36.21; most accessible tissue: Callus, score: 80.939	N	N	N	N
vg0619747679	T -> C	LOC_Os06g33940.2	upstream_gene_variant ; 1222.0bp to feature; MODIFIER	silent_mutation	Average:36.21; most accessible tissue: Callus, score: 80.939	N	N	N	N
vg0619747679	T -> C	LOC_Os06g33940-LOC_Os06g33950	intergenic_region ; MODIFIER	silent_mutation	Average:36.21; most accessible tissue: Callus, score: 80.939	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619747679	NA	1.97E-10	mr1057_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
vg0619747679	NA	1.57E-08	mr1062_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
vg0619747679	NA	4.17E-07	mr1126_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
vg0619747679	6.43E-07	1.28E-09	mr1127_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
vg0619747679	8.67E-06	8.67E-06	mr1127_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
vg0619747679	NA	1.27E-07	mr1167_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
vg0619747679	6.25E-06	1.17E-08	mr1456_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
vg0619747679	NA	2.94E-06	mr1544_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
vg0619747679	NA	2.96E-06	mr1565_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
vg0619747679	NA	1.21E-07	mr1726_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
vg0619747679	NA	3.04E-06	mr1736_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
vg0619747679	NA	3.46E-06	mr1736_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
vg0619747679	NA	3.46E-06	mr1781_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
vg0619747679	NA	5.50E-09	mr1829_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
vg0619747679	9.91E-06	9.91E-06	mr1914_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