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Detailed information for vg0724502952:

Variant ID: vg0724502952 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24502952
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTATAAGGGTCTCCAGATGCAAGAAGCACCCAAACAATCCAGATTTTTACCCAGACTCGAAAATGCTGGGTAGGTGTAAAATCTAGAAAATAAACTAGAA[G/A]
CAAGAAGCTGAGTAGCTTCTTCGCATTAACATCATACTTACATGTCTAGTTCGAACCTCAATGTTCGAAACTCTTTTCCTCAGCAAAAAGAAAAAAATGA

Reverse complement sequence

TCATTTTTTTCTTTTTGCTGAGGAAAAGAGTTTCGAACATTGAGGTTCGAACTAGACATGTAAGTATGATGTTAATGCGAAGAAGCTACTCAGCTTCTTG[C/T]
TTCTAGTTTATTTTCTAGATTTTACACCTACCCAGCATTTTCGAGTCTGGGTAAAAATCTGGATTGTTTGGGTGCTTCTTGCATCTGGAGACCCTTATAA

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	92.10%	7.30%	0.17%	0.51%	NA
All Indica	2759	98.80%	1.10%	0.04%	0.14%	NA
All Japonica	1512	98.00%	1.90%	0.07%	0.00%	NA
Aus	269	16.70%	77.00%	0.74%	5.58%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	99.20%	0.80%	0.00%	0.00%	NA
Indica Intermediate	786	96.70%	2.80%	0.13%	0.38%	NA
Temperate Japonica	767	97.30%	2.70%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.30%	3.30%	0.41%	0.00%	NA
VI/Aromatic	96	20.80%	72.90%	4.17%	2.08%	NA
Intermediate	90	87.80%	8.90%	0.00%	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
vg0724502952	G -> DEL	N	N	silent_mutation	Average:54.018; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg0724502952	G -> A	LOC_Os07g40940.1	upstream_gene_variant ; 2214.0bp to feature; MODIFIER	silent_mutation	Average:54.018; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg0724502952	G -> A	LOC_Os07g40930-LOC_Os07g40940	intergenic_region ; MODIFIER	silent_mutation	Average:54.018; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724502952	NA	1.71E-12	mr1231	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
vg0724502952	5.35E-06	NA	mr1354	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
vg0724502952	NA	1.44E-07	mr1415	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
vg0724502952	NA	6.32E-39	mr1549	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
vg0724502952	NA	4.54E-47	mr1550	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
vg0724502952	NA	1.44E-07	mr1567	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
vg0724502952	5.37E-08	NA	mr1829	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
vg0724502952	NA	1.08E-06	mr1126_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
vg0724502952	NA	7.15E-09	mr1347_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
vg0724502952	NA	8.97E-49	mr1550_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
vg0724502952	NA	1.48E-08	mr1567_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
vg0724502952	NA	2.48E-26	mr1757_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
vg0724502952	3.49E-13	NA	mr1829_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
vg0724502952	2.14E-11	NA	mr1842_2	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
vg0724502952	7.70E-07	NA	mr1902_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