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Detailed information for vg0108457524:

Variant ID: vg0108457524 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 8457524
Reference Allele: G	Alternative Allele: C,T
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCATGAAAGTGAAAGACACCCATGACAATCAACACACGCCTACCAGAAGCCACAACATACAAGCCTACATACGCCAAGACACGCCGCCGGATATCGACTT[G/C,T]
AAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTCGCCGGGCACAGATTCGAGGAGGAAG

Reverse complement sequence

CTTCCTCCTCGAATCTGTGCCCGGCGAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTT[C/G,A]
AAGTCGATATCCGGCGGCGTGTCTTGGCGTATGTAGGCTTGTATGTTGTGGCTTCTGGTAGGCGTGTGTTGATTGTCATGGGTGTCTTTCACTTTCATGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.70%	7.20%	0.02%	0.00%	NA
All Indica	2759	96.20%	3.80%	0.00%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	14.50%	85.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	95.10%	4.90%	0.00%	0.00%	NA
Indica Intermediate	786	93.90%	6.10%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	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
vg0108457524	G -> T	LOC_Os01g15070.1	missense_variant ; p.Leu33Phe; MODERATE	N	Average:58.973; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg0108457524	G -> T	LOC_Os01g15080.1	upstream_gene_variant ; 435.0bp to feature; MODIFIER	N	Average:58.973; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg0108457524	G -> T	LOC_Os01g15090.1	upstream_gene_variant ; 3548.0bp to feature; MODIFIER	N	Average:58.973; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg0108457524	G -> T	LOC_Os01g15060.1	downstream_gene_variant ; 1502.0bp to feature; MODIFIER	N	Average:58.973; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg0108457524	G -> C	LOC_Os01g15070.1	missense_variant ; p.Leu33Phe; MODERATE	nonsynonymous_codon ; L33F	Average:58.973; most accessible tissue: Minghui63 young leaf, score: 71.254	benign	-1.293	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0108457524	NA	6.45E-20	mr1095_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