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Detailed information for vg0217713261:

Variant ID: vg0217713261 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17713261
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAGGACCGTTTCAGATTTACAAAGTTGTGTCCAAAGGGGCTTATATGTTGCAAGGACTTGATGGTGAAGTTTATGGACGAGCACTTAATGGAAAATAT[T/C]
TGAAGAAATACTACCCAAGTGTTTGGATTAATTCATGATCGGCTGAGTGATGCCGATACATGTCAGCCGATGTGTTGACATCGCCTTTAGATTGCCGATA

Reverse complement sequence

TATCGGCAATCTAAAGGCGATGTCAACACATCGGCTGACATGTATCGGCATCACTCAGCCGATCATGAATTAATCCAAACACTTGGGTAGTATTTCTTCA[A/G]
ATATTTTCCATTAAGTGCTCGTCCATAAACTTCACCATCAAGTCCTTGCAACATATAAGCCCCTTTGGACACAACTTTGTAAATCTGAAACGGTCCTTCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.20%	3.30%	2.16%	1.33%	NA
All Indica	2759	91.60%	4.90%	2.90%	0.65%	NA
All Japonica	1512	99.70%	0.10%	0.07%	0.20%	NA
Aus	269	85.10%	6.70%	5.58%	2.60%	NA
Indica I	595	90.60%	5.90%	3.36%	0.17%	NA
Indica II	465	91.20%	6.50%	2.37%	0.00%	NA
Indica III	913	92.80%	3.30%	2.74%	1.20%	NA
Indica Intermediate	786	91.20%	5.00%	3.05%	0.76%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	62.50%	0.00%	4.17%	33.33%	NA
Intermediate	90	92.20%	2.20%	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
vg0217713261	T -> DEL	LOC_Os02g29760.1	N	frameshift_variant	Average:36.226; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg0217713261	T -> C	LOC_Os02g29760.1	synonymous_variant ; p.Leu1396Leu; LOW	synonymous_codon	Average:36.226; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217713261	NA	2.33E-06	mr1089	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
vg0217713261	NA	9.28E-09	mr1093	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
vg0217713261	NA	1.46E-08	mr1322_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
vg0217713261	NA	3.14E-13	mr1325_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
vg0217713261	NA	1.54E-13	mr1326_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
vg0217713261	NA	7.58E-23	mr1386_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
vg0217713261	NA	3.62E-07	mr1623_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
vg0217713261	3.62E-06	3.62E-06	mr1957_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