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Detailed information for vg0713013502:

Variant ID: vg0713013502 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13013502
Reference Allele: A	Alternative Allele: C,G,T
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCGCGGGATCCAGTCGCAGGAGCAGGGGTCACGACGAGCGATCTGTCCATTCGCCTCCCGAACGACACAGGGAGCGTCGAGTTGAACGACCTCGTAGGC[A/C,G,T]
CCCCATCGATCTTCGCGATACCATCAACCAGCGCCGCGCGGCAAGAGGCTGTGCTCCCAACCATTCACCAGACCGCTACGACGACGACGTGGATGGAGTT

Reverse complement sequence

AACTCCATCCACGTCGTCGTCGTAGCGGTCTGGTGAATGGTTGGGAGCACAGCCTCTTGCCGCGCGGCGCTGGTTGATGGTATCGCGAAGATCGATGGGG[T/G,C,A]
GCCTACGAGGTCGTTCAACTCGACGCTCCCTGTGTCGTTCGGGAGGCGAATGGACAGATCGCTCGTCGTGACCCCTGCTCCTGCGACTGGATCCCGCGCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.60%	0.10%	1.48%	6.75%	NA
All Indica	2759	90.40%	0.30%	1.99%	7.39%	NA
All Japonica	1512	91.70%	0.00%	0.99%	7.28%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	98.50%	0.00%	1.34%	0.17%	NA
Indica II	465	82.40%	0.40%	3.01%	14.19%	NA
Indica III	913	89.70%	0.20%	1.86%	8.21%	NA
Indica Intermediate	786	89.70%	0.40%	2.04%	7.89%	NA
Temperate Japonica	767	84.50%	0.00%	1.96%	13.56%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	0.00%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713013502	A -> DEL	LOC_Os07g23070.1	N	frameshift_variant	Average:61.568; most accessible tissue: Zhenshan97 flag leaf, score: 80.799	N	N	N	N
vg0713013502	A -> G	LOC_Os07g23070.1	missense_variant ; p.His275Arg; MODERATE	N	Average:61.568; most accessible tissue: Zhenshan97 flag leaf, score: 80.799	N	N	N	N
vg0713013502	A -> G	LOC_Os07g23060.1	upstream_gene_variant ; 2415.0bp to feature; MODIFIER	N	Average:61.568; most accessible tissue: Zhenshan97 flag leaf, score: 80.799	N	N	N	N
vg0713013502	A -> T	LOC_Os07g23070.1	missense_variant ; p.His275Leu; MODERATE	N	Average:61.568; most accessible tissue: Zhenshan97 flag leaf, score: 80.799	N	N	N	N
vg0713013502	A -> T	LOC_Os07g23060.1	upstream_gene_variant ; 2415.0bp to feature; MODIFIER	N	Average:61.568; most accessible tissue: Zhenshan97 flag leaf, score: 80.799	N	N	N	N
vg0713013502	A -> C	LOC_Os07g23070.1	missense_variant ; p.His275Pro; MODERATE	nonsynonymous_codon ; H275P	Average:61.568; most accessible tissue: Zhenshan97 flag leaf, score: 80.799	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713013502	2.04E-06	4.29E-07	mr1010	Ind_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