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Detailed information for vg0232065371:

Variant ID: vg0232065371 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 32065371
Reference Allele: T	Alternative Allele: C,TC,TTC
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.74, C: 0.26, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

ATTGAATTCGCTCTTAGGGAGAACAACACAGGATCGTTCCCTCGAGGCTTGTCTCTGATGCTTCGTTCGATTGTATGAACTCATCACTCTTTTTTTTTTT[T/C,TC,TTC]
CCATTTTGAAATAAAAGTACAGATGTGTTTGGACATACTCATGATTCTTTGTCACAAACATTTTCAGGGAAAATGGATATATGACATGGACCCTTTTGAG

Reverse complement sequence

CTCAAAAGGGTCCATGTCATATATCCATTTTCCCTGAAAATGTTTGTGACAAAGAATCATGAGTATGTCCAAACACATCTGTACTTTTATTTCAAAATGG[A/G,GA,GAA]
AAAAAAAAAAAGAGTGATGAGTTCATACAATCGAACGAAGCATCAGAGACAAGCCTCGAGGGAACGATCCTGTGTTGTTCTCCCTAAGAGCGAATTCAAT

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	61.20%	35.50%	0.36%	0.00%	TTC: 2.18%; TC: 0.76%
All Indica	2759	93.60%	1.00%	0.54%	0.00%	TTC: 3.70%; TC: 1.16%
All Japonica	1512	0.50%	99.50%	0.00%	0.00%	NA
Aus	269	94.10%	3.30%	0.74%	0.00%	TC: 1.49%; TTC: 0.37%
Indica I	595	98.70%	0.30%	0.17%	0.00%	TTC: 0.67%; TC: 0.17%
Indica II	465	95.30%	1.30%	0.00%	0.00%	TTC: 3.01%; TC: 0.43%
Indica III	913	94.90%	0.90%	0.66%	0.00%	TC: 2.63%; TTC: 0.99%
Indica Intermediate	786	87.30%	1.50%	1.02%	0.00%	TTC: 9.54%; TC: 0.64%
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	0.00%	100.00%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	42.20%	57.80%	0.00%	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
vg0232065371	T -> TC	LOC_Os02g52390.1	intron_variant ; MODIFIER	silent_mutation	Average:40.696; most accessible tissue: Callus, score: 52.423	N	N	N	N
vg0232065371	T -> TTC	LOC_Os02g52390.1	intron_variant ; MODIFIER	silent_mutation	Average:40.696; most accessible tissue: Callus, score: 52.423	N	N	N	N
vg0232065371	T -> C	LOC_Os02g52390.1	intron_variant ; MODIFIER	silent_mutation	Average:40.696; most accessible tissue: Callus, score: 52.423	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232065371	NA	1.47E-29	mr1202	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
vg0232065371	NA	1.64E-51	mr1795	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
vg0232065371	NA	6.24E-07	mr1915	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
vg0232065371	NA	8.42E-15	mr1982	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
vg0232065371	NA	5.15E-08	mr1982	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
vg0232065371	NA	1.16E-17	mr1146_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
vg0232065371	NA	3.85E-18	mr1239_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
vg0232065371	NA	2.20E-06	mr1533_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
vg0232065371	NA	3.05E-12	mr1553_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
vg0232065371	NA	2.10E-06	mr1980_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