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Detailed information for vg0608141426:

Variant ID: vg0608141426 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8141426
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCCCTGATCAGATGAAAAGGAGGCCCAGGCCTAAGAAGAGAGAGGGAGAGGGGGTGGGACTCTGGCGAACGGGTTCTAGAGCCTGAACTCTCTCTCGCT[C/A]
TCCGGCTCTATGTGATTCCTTCACACACAGATCCACCAGAACACAGGAGTAGGGTGTTACGCTTCTCAGCGGCCCGAACCTGTCTACGTCGCCCGTGTCT

Reverse complement sequence

AGACACGGGCGACGTAGACAGGTTCGGGCCGCTGAGAAGCGTAACACCCTACTCCTGTGTTCTGGTGGATCTGTGTGTGAAGGAATCACATAGAGCCGGA[G/T]
AGCGAGAGAGAGTTCAGGCTCTAGAACCCGTTCGCCAGAGTCCCACCCCCTCTCCCTCTCTCTTCTTAGGCCTGGGCCTCCTTTTCATCTGATCAGGGGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.80%	1.40%	3.07%	25.71%	NA
All Indica	2759	71.00%	0.00%	1.52%	27.51%	NA
All Japonica	1512	77.50%	4.40%	3.57%	14.55%	NA
Aus	269	14.50%	0.00%	15.99%	69.52%	NA
Indica I	595	58.00%	0.00%	1.34%	40.67%	NA
Indica II	465	94.20%	0.00%	0.43%	5.38%	NA
Indica III	913	62.30%	0.00%	2.41%	35.27%	NA
Indica Intermediate	786	77.10%	0.00%	1.27%	21.63%	NA
Temperate Japonica	767	61.80%	8.10%	6.00%	24.12%	NA
Tropical Japonica	504	99.00%	0.00%	0.79%	0.20%	NA
Japonica Intermediate	241	82.60%	1.70%	1.66%	14.11%	NA
VI/Aromatic	96	52.10%	1.00%	5.21%	41.67%	NA
Intermediate	90	88.90%	0.00%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608141426	C -> A	LOC_Os06g14480.1	upstream_gene_variant ; 173.0bp to feature; MODIFIER	silent_mutation	Average:42.978; most accessible tissue: Zhenshan97 root, score: 86.79	N	N	N	N
vg0608141426	C -> A	LOC_Os06g14490.1	upstream_gene_variant ; 1225.0bp to feature; MODIFIER	silent_mutation	Average:42.978; most accessible tissue: Zhenshan97 root, score: 86.79	N	N	N	N
vg0608141426	C -> A	LOC_Os06g14490.2	upstream_gene_variant ; 1225.0bp to feature; MODIFIER	silent_mutation	Average:42.978; most accessible tissue: Zhenshan97 root, score: 86.79	N	N	N	N
vg0608141426	C -> A	LOC_Os06g14480-LOC_Os06g14490	intergenic_region ; MODIFIER	silent_mutation	Average:42.978; most accessible tissue: Zhenshan97 root, score: 86.79	N	N	N	N
vg0608141426	C -> DEL	N	N	silent_mutation	Average:42.978; most accessible tissue: Zhenshan97 root, score: 86.79	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608141426	4.10E-08	2.20E-10	mr1549_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
vg0608141426	1.44E-06	1.20E-09	mr1757_2	Jap_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