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Detailed information for vg1217216616:

Variant ID: vg1217216616 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17216616
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TCTGATCTTACGTCAATCAAGCAAAAGCATGATGAGCCAGTGCAAGAGTATATTCAAAGGTTCAGGGAAATGAGGAATAAATGTTACAGCTTGAGTTTGA[C/T]
CGATGCCCAGCTAGCCGATTTGGCGTTTCAAGGGATGATTGCTCCGATCAGGGAAAAATTCTCATATGAAGATTTCGAAAGTTTGTCGCATCTTACACAG

Reverse complement sequence

CTGTGTAAGATGCGACAAACTTTCGAAATCTTCATATGAGAATTTTTCCCTGATCGGAGCAATCATCCCTTGAAACGCCAAATCGGCTAGCTGGGCATCG[G/A]
TCAAACTCAAGCTGTAACATTTATTCCTCATTTCCCTGAACCTTTGAATATACTCTTGCACTGGCTCATCATGCTTTTGCTTGATTGACGTAAGATCAGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.60%	22.70%	3.17%	4.53%	NA
All Indica	2759	58.50%	30.40%	3.91%	7.21%	NA
All Japonica	1512	83.90%	12.70%	2.58%	0.86%	NA
Aus	269	94.10%	4.50%	0.74%	0.74%	NA
Indica I	595	22.70%	57.60%	6.39%	13.28%	NA
Indica II	465	65.60%	26.00%	3.87%	4.52%	NA
Indica III	913	75.00%	19.10%	1.53%	4.38%	NA
Indica Intermediate	786	62.10%	25.60%	4.83%	7.51%	NA
Temperate Japonica	767	97.50%	0.70%	0.52%	1.30%	NA
Tropical Japonica	504	63.70%	30.60%	5.75%	0.00%	NA
Japonica Intermediate	241	82.60%	13.70%	2.49%	1.24%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	1.11%	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
vg1217216616	C -> DEL	LOC_Os12g29070.1	N	frameshift_variant	Average:37.464; most accessible tissue: Minghui63 flag leaf, score: 59.912	N	N	N	N
vg1217216616	C -> T	LOC_Os12g29070.1	missense_variant ; p.Thr583Ile; MODERATE	nonsynonymous_codon ; T583I	Average:37.464; most accessible tissue: Minghui63 flag leaf, score: 59.912	benign	0.738	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217216616	NA	8.17E-06	mr1124	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
vg1217216616	NA	8.50E-06	mr1218	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
vg1217216616	3.84E-06	NA	mr1422	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
vg1217216616	NA	1.15E-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
vg1217216616	NA	8.51E-06	mr1511	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
vg1217216616	NA	2.34E-08	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
vg1217216616	NA	5.48E-09	mr1707	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
vg1217216616	9.77E-06	NA	mr1083_2	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
vg1217216616	5.98E-06	NA	mr1132_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
vg1217216616	5.92E-06	NA	mr1132_2	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
vg1217216616	4.55E-06	NA	mr1226_2	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
vg1217216616	NA	3.87E-06	mr1659_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
vg1217216616	NA	3.80E-06	mr1850_2	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
vg1217216616	4.21E-06	9.92E-06	mr1986_2	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