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Detailed information for vg1207088249:

Variant ID: vg1207088249 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7088249
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTATTCATACGTTATTGGTAAATTAAAGATCTAAAATATTCTTTTGACACCATATTGATGTTCTTTATCTCCTACTTAGCCTTCATTCCATCTAGCTC[A/T]
TTCATTGAGGTCACATGAAAAGATGCACTTCAATAGCGCAAGATTAATTAATTATTAAATATTACAAACTCAAAAGTGAATTTATTTGATTTTTATAAAA

Reverse complement sequence

TTTTATAAAAATCAAATAAATTCACTTTTGAGTTTGTAATATTTAATAATTAATTAATCTTGCGCTATTGAAGTGCATCTTTTCATGTGACCTCAATGAA[T/A]
GAGCTAGATGGAATGAAGGCTAAGTAGGAGATAAAGAACATCAATATGGTGTCAAAAGAATATTTTAGATCTTTAATTTACCAATAACGTATGAATAGAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.00%	9.30%	1.86%	13.90%	NA
All Indica	2759	97.00%	1.00%	1.09%	0.91%	NA
All Japonica	1512	36.60%	23.80%	1.79%	37.83%	NA
Aus	269	67.70%	15.20%	5.95%	11.15%	NA
Indica I	595	99.20%	0.20%	0.17%	0.50%	NA
Indica II	465	93.30%	1.30%	4.09%	1.29%	NA
Indica III	913	97.90%	1.00%	0.66%	0.44%	NA
Indica Intermediate	786	96.60%	1.40%	0.51%	1.53%	NA
Temperate Japonica	767	41.20%	2.60%	2.09%	54.11%	NA
Tropical Japonica	504	20.40%	61.90%	1.59%	16.07%	NA
Japonica Intermediate	241	55.60%	11.60%	1.24%	31.54%	NA
VI/Aromatic	96	79.20%	1.00%	9.38%	10.42%	NA
Intermediate	90	61.10%	10.00%	6.67%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207088249	A -> DEL	N	N	silent_mutation	Average:27.968; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1207088249	A -> T	LOC_Os12g12840-LOC_Os12g12850	intergenic_region ; MODIFIER	silent_mutation	Average:27.968; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207088249	1.09E-06	NA	mr1236	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
vg1207088249	NA	2.25E-06	mr1304	Jap_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
vg1207088249	NA	1.26E-06	mr1345	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
vg1207088249	NA	3.30E-06	mr1382	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
vg1207088249	NA	2.45E-06	mr1382	Jap_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
vg1207088249	NA	2.77E-06	mr1417	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
vg1207088249	NA	1.98E-06	mr1422	Jap_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
vg1207088249	NA	9.72E-06	mr1485	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
vg1207088249	NA	2.57E-07	mr1583	Jap_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
vg1207088249	NA	7.06E-06	mr1633	Jap_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
vg1207088249	NA	4.77E-07	mr1696	Jap_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
vg1207088249	NA	7.11E-08	mr1697	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
vg1207088249	1.17E-06	NA	mr1960	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