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Detailed information for vg0715972024:

Variant ID: vg0715972024 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15972024
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

AATCTACTCGATCGGCTGTAGATATTAATGACATATAATCCTTACATCGATATATACTTAAATCAAGTGATTGGGATAGATCGATCACCTTGCCGAGACA[G/A]
TATAAATCACTTAGATCGAAATATATATTAATAGTGAGATTATATATATTCATAGCATAGCCGATCAGATAGATCTAGCATGTATCGGCTAGTACTCCGA

Reverse complement sequence

TCGGAGTACTAGCCGATACATGCTAGATCTATCTGATCGGCTATGCTATGAATATATATAATCTCACTATTAATATATATTTCGATCTAAGTGATTTATA[C/T]
TGTCTCGGCAAGGTGATCGATCTATCCCAATCACTTGATTTAAGTATATATCGATGTAAGGATTATATGTCATTAATATCTACAGCCGATCGAGTAGATT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.70%	1.90%	0.21%	1.12%	NA
All Indica	2759	97.80%	0.10%	0.33%	1.85%	NA
All Japonica	1512	93.80%	6.00%	0.07%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	89.90%	0.00%	0.65%	9.46%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.20%	0.30%	0.64%	0.89%	NA
Temperate Japonica	767	89.20%	10.60%	0.00%	0.26%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0715972024	G -> DEL	N	N	silent_mutation	Average:11.254; most accessible tissue: Callus, score: 27.667	N	N	N	N
vg0715972024	G -> A	LOC_Os07g27420.1	upstream_gene_variant ; 1202.0bp to feature; MODIFIER	silent_mutation	Average:11.254; most accessible tissue: Callus, score: 27.667	N	N	N	N
vg0715972024	G -> A	LOC_Os07g27410.1	downstream_gene_variant ; 1391.0bp to feature; MODIFIER	silent_mutation	Average:11.254; most accessible tissue: Callus, score: 27.667	N	N	N	N
vg0715972024	G -> A	LOC_Os07g27410-LOC_Os07g27420	intergenic_region ; MODIFIER	silent_mutation	Average:11.254; most accessible tissue: Callus, score: 27.667	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715972024	1.49E-06	1.49E-06	mr1528_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