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Detailed information for vg0724212535:

Variant ID: vg0724212535 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24212535
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.69, G: 0.32, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

GAGGGCCTACCATGTATCGTCCAGTTCTAGTGGTTCTTCAGTAGTTTCCTAGCTAACTTTCGGGTCCTTAGTTATCATCAGACATAGGTGTCTATCGTCT[A/G]
TCAGTATTTTAGTGTTCTAGCTTTATTATCCATGTAACTCTGGAGTGATGAGGGAACAGCATGTCGATCCTGGCATCTTCAGGTGTAGGTTCTCTAGTAG

Reverse complement sequence

CTACTAGAGAACCTACACCTGAAGATGCCAGGATCGACATGCTGTTCCCTCATCACTCCAGAGTTACATGGATAATAAAGCTAGAACACTAAAATACTGA[T/C]
AGACGATAGACACCTATGTCTGATGATAACTAAGGACCCGAAAGTTAGCTAGGAAACTACTGAAGAACCACTAGAACTGGACGATACATGGTAGGCCCTC

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	58.10%	41.50%	0.11%	0.34%	NA
All Indica	2759	91.80%	7.80%	0.11%	0.33%	NA
All Japonica	1512	0.70%	99.10%	0.00%	0.20%	NA
Aus	269	44.60%	55.40%	0.00%	0.00%	NA
Indica I	595	93.10%	6.40%	0.17%	0.34%	NA
Indica II	465	88.00%	11.60%	0.00%	0.43%	NA
Indica III	913	97.00%	2.70%	0.00%	0.22%	NA
Indica Intermediate	786	87.00%	12.30%	0.25%	0.38%	NA
Temperate Japonica	767	0.70%	99.20%	0.00%	0.13%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	97.50%	0.00%	0.83%	NA
VI/Aromatic	96	44.80%	54.20%	0.00%	1.04%	NA
Intermediate	90	43.30%	51.10%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0724212535	A -> DEL	N	N	silent_mutation	Average:77.604; most accessible tissue: Callus, score: 99.911	N	N	N	N
vg0724212535	A -> G	LOC_Os07g40380.1	3_prime_UTR_variant ; 191.0bp to feature; MODIFIER	silent_mutation	Average:77.604; most accessible tissue: Callus, score: 99.911	N	N	N	N
vg0724212535	A -> G	LOC_Os07g40370.1	upstream_gene_variant ; 4570.0bp to feature; MODIFIER	silent_mutation	Average:77.604; most accessible tissue: Callus, score: 99.911	N	N	N	N
vg0724212535	A -> G	LOC_Os07g40390.1	downstream_gene_variant ; 3343.0bp to feature; MODIFIER	silent_mutation	Average:77.604; most accessible tissue: Callus, score: 99.911	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724212535	NA	9.69E-07	mr1082	Ind_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
vg0724212535	NA	2.91E-27	mr1181	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
vg0724212535	NA	1.13E-31	mr1213	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
vg0724212535	NA	8.88E-07	mr1408	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
vg0724212535	NA	2.55E-07	mr1761	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
vg0724212535	NA	8.13E-33	mr1878	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
vg0724212535	NA	2.24E-06	mr1181_2	Ind_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
vg0724212535	NA	1.66E-08	mr1319_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