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Detailed information for vg0500335511:

Variant ID: vg0500335511 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 335511
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGTTCAGCAAAAAGTATCTCGAGATACCAAATCGTTTCCGATCGTTGAATCGTTTCCGATCATTCAACGATCGGAAACGATTTGATATCGTAAGATACA[G/A]
GTACCTCGATATATTTTTTGTTAGACCGGAGCAAATCTCCCTAAATTGTACCTAGATGATATATCAGTCGAGCATTCTCGAATGAGTCATTAAGTTTATC

Reverse complement sequence

GATAAACTTAATGACTCATTCGAGAATGCTCGACTGATATATCATCTAGGTACAATTTAGGGAGATTTGCTCCGGTCTAACAAAAAATATATCGAGGTAC[C/T]
TGTATCTTACGATATCAAATCGTTTCCGATCGTTGAATGATCGGAAACGATTCAACGATCGGAAACGATTTGGTATCTCGAGATACTTTTTGCTGAACTG

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	70.50%	29.10%	0.36%	0.00%	NA
All Indica	2759	90.90%	8.90%	0.18%	0.00%	NA
All Japonica	1512	32.00%	67.50%	0.53%	0.00%	NA
Aus	269	68.00%	31.20%	0.74%	0.00%	NA
Indica I	595	88.60%	11.30%	0.17%	0.00%	NA
Indica II	465	88.40%	11.40%	0.22%	0.00%	NA
Indica III	913	90.60%	9.30%	0.11%	0.00%	NA
Indica Intermediate	786	94.50%	5.20%	0.25%	0.00%	NA
Temperate Japonica	767	20.10%	79.10%	0.78%	0.00%	NA
Tropical Japonica	504	56.00%	43.70%	0.40%	0.00%	NA
Japonica Intermediate	241	19.90%	80.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	28.90%	2.22%	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
vg0500335511	G -> A	LOC_Os05g01570.1	upstream_gene_variant ; 3335.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500335511	G -> A	LOC_Os05g01560-LOC_Os05g01570	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0500335511	2.60E-06	NA	mr1248	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