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Detailed information for vg0217652051:

Variant ID: vg0217652051 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17652051
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCGGGGACCAGTTCTTCTAAGGATGGAGATGGGAAACAAGCTCCAGACGGCTCGGCTCAGCTGAGTAACAAAAGTGCTACCGACAGCTCTCTAGGAAAT[C/T]
AAGGTGACAATTCTCAAGGAGTCCATGGAGTGCAAGGTGACGGGGTGCATGGAGTTCAAGGTGGTGGTGCCCGAGGGTTGCAAGGAGGGGATCTTAATCA

Reverse complement sequence

TGATTAAGATCCCCTCCTTGCAACCCTCGGGCACCACCACCTTGAACTCCATGCACCCCGTCACCTTGCACTCCATGGACTCCTTGAGAATTGTCACCTT[G/A]
ATTTCCTAGAGAGCTGTCGGTAGCACTTTTGTTACTCAGCTGAGCCGAGCCGTCTGGAGCTTGTTTCCCATCTCCATCCTTAGAAGAACTGGTCCCCGGA

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	82.40%	11.60%	5.40%	0.61%	NA
All Indica	2759	77.00%	14.70%	7.25%	1.05%	NA
All Japonica	1512	99.60%	0.10%	0.33%	0.00%	NA
Aus	269	33.80%	50.90%	15.24%	0.00%	NA
Indica I	595	85.70%	1.20%	11.76%	1.34%	NA
Indica II	465	95.30%	1.70%	3.01%	0.00%	NA
Indica III	913	60.70%	33.30%	4.27%	1.75%	NA
Indica Intermediate	786	78.50%	11.10%	9.80%	0.64%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	95.80%	0.00%	4.17%	0.00%	NA
Intermediate	90	92.20%	2.20%	5.56%	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
vg0217652051	C -> T	LOC_Os02g29650.1	stop_gained ; p.Gln117*; HIGH	stop_gained	Average:32.835; most accessible tissue: Minghui63 flag leaf, score: 69.681	N	N	N	N
vg0217652051	C -> DEL	LOC_Os02g29650.1	N	frameshift_variant	Average:32.835; most accessible tissue: Minghui63 flag leaf, score: 69.681	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217652051	NA	5.30E-06	mr1054	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
vg0217652051	4.50E-07	4.50E-07	mr1275	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
vg0217652051	NA	2.62E-06	mr1286	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
vg0217652051	NA	3.03E-06	mr1345	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
vg0217652051	1.75E-06	1.75E-06	mr1345	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
vg0217652051	NA	1.13E-06	mr1427	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
vg0217652051	NA	7.79E-06	mr1427	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
vg0217652051	NA	2.14E-06	mr1433	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
vg0217652051	NA	6.20E-06	mr1474	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
vg0217652051	NA	6.20E-06	mr1475	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
vg0217652051	1.93E-06	1.93E-06	mr1700	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
vg0217652051	NA	1.64E-06	mr1777	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
vg0217652051	2.02E-06	2.02E-06	mr1777	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
vg0217652051	NA	4.35E-06	mr1972	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
vg0217652051	3.11E-07	3.11E-07	mr1972	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