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Detailed information for vg0616953325:

Variant ID: vg0616953325 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 16953325
Reference Allele: G	Alternative Allele: GTCA,A
Primary Allele: GTCA	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

AATTTGGATTGACCACATGTTTTTTTGATTGGCTGCAATTAATAAGCATGAAATAGGGACTGCATATGAATTTTGAACTGACTACAATAAAGCTATCTTC[G/GTCA,A]
TCATCAAGGGGAATGGCATCATTGTAATCTACCTTCCTTTTGTTTGACTTGTCAAGCTGCTCCAAATATGCATGCCACTTTGGTTGGTTTTTAAGTTCAT

Reverse complement sequence

ATGAACTTAAAAACCAACCAAAGTGGCATGCATATTTGGAGCAGCTTGACAAGTCAAACAAAAGGAAGGTAGATTACAATGATGCCATTCCCCTTGATGA[C/TGAC,T]
GAAGATAGCTTTATTGTAGTCAGTTCAAAATTCATATGCAGTCCCTATTTCATGCTTATTAATTGCAGCCAATCAAAAAAACATGTGGTCAATCCAAATT

Allele Frequencies:

Populations	Population Size	Frequency of GTCA(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.50%	29.40%	0.08%	0.00%	A: 5.99%
All Indica	2759	97.60%	1.70%	0.04%	0.00%	A: 0.58%
All Japonica	1512	2.80%	86.60%	0.00%	0.00%	A: 10.65%
Aus	269	91.40%	1.90%	0.00%	0.00%	A: 6.69%
Indica I	595	97.50%	2.50%	0.00%	0.00%	NA
Indica II	465	97.40%	1.10%	0.00%	0.00%	A: 1.51%
Indica III	913	99.20%	0.20%	0.11%	0.00%	A: 0.44%
Indica Intermediate	786	96.10%	3.30%	0.00%	0.00%	A: 0.64%
Temperate Japonica	767	3.50%	96.20%	0.00%	0.00%	A: 0.26%
Tropical Japonica	504	2.00%	70.00%	0.00%	0.00%	A: 27.98%
Japonica Intermediate	241	2.10%	90.50%	0.00%	0.00%	A: 7.47%
VI/Aromatic	96	17.70%	1.00%	0.00%	0.00%	A: 81.25%
Intermediate	90	55.60%	30.00%	3.33%	0.00%	A: 11.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0616953325	G -> A	LOC_Os06g29580.1	intron_variant ; MODIFIER	silent_mutation	Average:43.505; most accessible tissue: Callus, score: 61.918	N	N	N	N
vg0616953325	G -> GTCA	LOC_Os06g29580.1	intron_variant ; MODIFIER	silent_mutation	Average:43.505; most accessible tissue: Callus, score: 61.918	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0616953325	NA	7.12E-08	mr1930	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
vg0616953325	8.58E-07	NA	mr1070_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
vg0616953325	1.93E-09	NA	mr1082_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
vg0616953325	2.25E-10	NA	mr1083_2	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
vg0616953325	4.50E-07	NA	mr1085_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
vg0616953325	1.59E-06	NA	mr1103_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
vg0616953325	7.62E-07	NA	mr1104_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
vg0616953325	1.89E-06	NA	mr1107_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
vg0616953325	2.48E-07	NA	mr1145_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
vg0616953325	1.29E-06	NA	mr1226_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
vg0616953325	3.52E-08	3.24E-09	mr1408_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