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Detailed information for vg0208128713:

Variant ID: vg0208128713 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 8128713
Reference Allele: T	Alternative Allele: C,TCC
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.53, T: 0.46, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGGTTGTGTGTATAGATCTAAAGTTTGGATCCAAACTTCAGTCATTTTCCAACACATTAACCTGTCATATAAACATAACTTTTCAGTCACATCATCTT[T/C,TCC]
AATTTTAACCAAAATCCAAACTTTGCGCTGACTAAACACAGACAGCCATAGTTTAAAATTGAGGTAAAATTGTTTTGATGTCCTGAGATATTTCTTGATA

Reverse complement sequence

TATCAAGAAATATCTCAGGACATCAAAACAATTTTACCTCAATTTTAAACTATGGCTGTCTGTGTTTAGTCAGCGCAAAGTTTGGATTTTGGTTAAAATT[A/G,GGA]
AAGATGATGTGACTGAAAAGTTATGTTTATATGACAGGTTAATGTGTTGGAAAATGACTGAAGTTTGGATCCAAACTTTAGATCTATACACACAACCTAT

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	56.00%	14.20%	3.64%	26.20%	TCC: 0.02%
All Indica	2759	57.40%	5.40%	5.44%	31.79%	TCC: 0.04%
All Japonica	1512	65.50%	31.70%	1.19%	1.59%	NA
Aus	269	1.50%	0.00%	0.00%	98.51%	NA
Indica I	595	87.10%	1.50%	5.88%	5.55%	NA
Indica II	465	31.60%	3.40%	8.60%	56.34%	NA
Indica III	913	50.70%	8.70%	1.42%	39.21%	NA
Indica Intermediate	786	57.90%	5.60%	7.89%	28.50%	TCC: 0.13%
Temperate Japonica	767	89.20%	9.00%	1.17%	0.65%	NA
Tropical Japonica	504	24.60%	72.20%	0.99%	2.18%	NA
Japonica Intermediate	241	75.50%	19.50%	1.66%	3.32%	NA
VI/Aromatic	96	22.90%	25.00%	0.00%	52.08%	NA
Intermediate	90	52.20%	18.90%	4.44%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208128713	T -> TCC	LOC_Os02g14720-LOC_Os02g14730	intergenic_region ; MODIFIER	silent_mutation	Average:81.347; most accessible tissue: Callus, score: 92.729	N	N	N	N
vg0208128713	T -> DEL	N	N	silent_mutation	Average:81.347; most accessible tissue: Callus, score: 92.729	N	N	N	N
vg0208128713	T -> C	LOC_Os02g14720-LOC_Os02g14730	intergenic_region ; MODIFIER	silent_mutation	Average:81.347; most accessible tissue: Callus, score: 92.729	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208128713	1.98E-06	9.28E-07	mr1484	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
vg0208128713	NA	1.20E-07	mr1530	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
vg0208128713	NA	2.96E-06	mr1530	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
vg0208128713	NA	7.11E-09	mr1557	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
vg0208128713	NA	1.47E-11	mr1593	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
vg0208128713	NA	3.84E-06	mr1598	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
vg0208128713	NA	3.22E-07	mr1742	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
vg0208128713	NA	3.17E-07	mr1502_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
vg0208128713	NA	6.02E-14	mr1593_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
vg0208128713	NA	7.52E-06	mr1892_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