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Detailed information for vg0101328049:

Variant ID: vg0101328049 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1328049
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGTTTGACCACTTGTCTTATTTAAAATTTTTTGAAATTATTAATTATTTTATTTATGGCTTACTTTATTATCTACAGTATTTTAAGCACAACTTTTCGT[T/G]
TTTTATATTTGTAAAAAAAATTGAATAAGACGAGTGGTCAAACGTTAGAAGCAAAAACCGAAAATCCCTTGTACCGTGGGGCGGAGGGAGTAGTAGAGTT

Reverse complement sequence

AACTCTACTACTCCCTCCGCCCCACGGTACAAGGGATTTTCGGTTTTTGCTTCTAACGTTTGACCACTCGTCTTATTCAATTTTTTTTACAAATATAAAA[A/C]
ACGAAAAGTTGTGCTTAAAATACTGTAGATAATAAAGTAAGCCATAAATAAAATAATTAATAATTTCAAAAAATTTTAAATAAGACAAGTGGTCAAACGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.10%	7.40%	0.36%	19.11%	NA
All Indica	2759	68.50%	2.90%	0.58%	27.94%	NA
All Japonica	1512	91.40%	0.30%	0.07%	8.27%	NA
Aus	269	11.90%	87.70%	0.00%	0.37%	NA
Indica I	595	73.90%	0.00%	0.67%	25.38%	NA
Indica II	465	95.30%	0.20%	0.00%	4.52%	NA
Indica III	913	52.50%	3.50%	0.66%	43.37%	NA
Indica Intermediate	786	67.30%	6.10%	0.76%	25.83%	NA
Temperate Japonica	767	88.10%	0.10%	0.13%	11.60%	NA
Tropical Japonica	504	98.60%	0.60%	0.00%	0.79%	NA
Japonica Intermediate	241	86.70%	0.00%	0.00%	13.28%	NA
VI/Aromatic	96	81.20%	17.70%	0.00%	1.04%	NA
Intermediate	90	78.90%	15.60%	0.00%	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
vg0101328049	T -> G	LOC_Os01g03270.1	upstream_gene_variant ; 123.0bp to feature; MODIFIER	silent_mutation	Average:58.694; most accessible tissue: Zhenshan97 panicle, score: 87.764	N	N	N	N
vg0101328049	T -> G	LOC_Os01g03280.1	downstream_gene_variant ; 2755.0bp to feature; MODIFIER	silent_mutation	Average:58.694; most accessible tissue: Zhenshan97 panicle, score: 87.764	N	N	N	N
vg0101328049	T -> G	LOC_Os01g03260-LOC_Os01g03270	intergenic_region ; MODIFIER	silent_mutation	Average:58.694; most accessible tissue: Zhenshan97 panicle, score: 87.764	N	N	N	N
vg0101328049	T -> DEL	N	N	silent_mutation	Average:58.694; most accessible tissue: Zhenshan97 panicle, score: 87.764	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101328049	NA	2.15E-10	mr1166_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
vg0101328049	NA	8.25E-20	mr1305_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
vg0101328049	NA	6.82E-07	mr1567_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
vg0101328049	NA	1.46E-07	mr1582_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
vg0101328049	NA	1.26E-15	mr1587_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
vg0101328049	NA	1.81E-28	mr1757_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
vg0101328049	NA	4.41E-10	mr1762_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
vg0101328049	NA	8.24E-08	mr1765_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
vg0101328049	2.72E-07	NA	mr1889_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
vg0101328049	8.22E-06	NA	mr1894_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
vg0101328049	5.93E-07	NA	mr1896_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
vg0101328049	NA	1.52E-10	mr1897_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
vg0101328049	6.50E-06	NA	mr1907_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
vg0101328049	NA	2.21E-07	mr1921_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
vg0101328049	NA	9.98E-06	mr1951_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