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Detailed information for vg0818212763:

Variant ID: vg0818212763 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 18212763
Reference Allele: AT	Alternative Allele: A,ATT,TT,ATTT
Primary Allele: AT	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGATTGTCCATCTTATTTGAAATTTTTTATAATTAGTATTTTTATTATTATGAGATGATAAAACATGAATAGTACTTTATGCGTGACTTATGTTTTTA[AT/A,ATT,TT,ATTT]
TTTTTTTTCAAAATTTTTTTAAATAAGACGGACGATTAAAGTTGGGCACAGAAAATCATGGCTGCACTTAAAATGGGACGGATGGAGTAATTATTTCTAA

Reverse complement sequence

TTAGAAATAATTACTCCATCCGTCCCATTTTAAGTGCAGCCATGATTTTCTGTGCCCAACTTTAATCGTCCGTCTTATTTAAAAAAATTTTGAAAAAAAA[AT/T,AAT,AA,AAAT]
TAAAAACATAAGTCACGCATAAAGTACTATTCATGTTTTATCATCTCATAATAATAAAAATACTAATTATAAAAAATTTCAAATAAGATGGACAATCAAA

Allele Frequencies:

Populations	Population Size	Frequency of AT(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.00%	30.40%	2.07%	1.02%	TT: 5.67%; ATT: 2.79%; ATTT: 0.04%
All Indica	2759	43.60%	51.10%	2.61%	0.33%	TT: 2.21%; ATT: 0.14%
All Japonica	1512	90.90%	0.20%	0.86%	0.00%	ATT: 8.00%; TT: 0.07%
Aus	269	10.80%	0.70%	3.35%	12.27%	TT: 72.49%; ATT: 0.37%
Indica I	595	56.10%	43.40%	0.34%	0.00%	TT: 0.17%
Indica II	465	84.10%	11.40%	3.23%	0.00%	TT: 1.29%
Indica III	913	18.90%	76.60%	2.30%	0.22%	TT: 1.86%; ATT: 0.11%
Indica Intermediate	786	38.70%	51.00%	4.33%	0.89%	TT: 4.71%; ATT: 0.38%
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	75.00%	0.00%	2.38%	0.00%	ATT: 22.62%
Japonica Intermediate	241	95.90%	0.40%	0.41%	0.00%	ATT: 2.90%; TT: 0.41%
VI/Aromatic	96	85.40%	1.00%	1.04%	3.12%	TT: 5.21%; ATTT: 2.08%; ATT: 2.08%
Intermediate	90	62.20%	20.00%	3.33%	3.33%	TT: 6.67%; ATT: 4.44%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818212763	AT -> DEL	N	N	silent_mutation	Average:36.388; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0818212763	AT -> ATTT	LOC_Os08g29650-LOC_Os08g29660	intergenic_region ; MODIFIER	silent_mutation	Average:36.388; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0818212763	AT -> A	LOC_Os08g29650-LOC_Os08g29660	intergenic_region ; MODIFIER	silent_mutation	Average:36.388; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0818212763	AT -> TT	LOC_Os08g29650-LOC_Os08g29660	intergenic_region ; MODIFIER	silent_mutation	Average:36.388; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0818212763	AT -> ATT	LOC_Os08g29650-LOC_Os08g29660	intergenic_region ; MODIFIER	silent_mutation	Average:36.388; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818212763	NA	4.12E-07	mr1004	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
vg0818212763	NA	5.70E-07	mr1028	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
vg0818212763	NA	3.52E-25	mr1095	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
vg0818212763	NA	2.59E-38	mr1098	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
vg0818212763	NA	8.99E-34	mr1099	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
vg0818212763	NA	1.03E-33	mr1101	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
vg0818212763	4.56E-07	2.69E-21	mr1113	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
vg0818212763	4.98E-08	9.38E-24	mr1114	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
vg0818212763	8.52E-07	2.05E-19	mr1116	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
vg0818212763	5.35E-09	1.64E-27	mr1117	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
vg0818212763	1.87E-07	2.09E-23	mr1119	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
vg0818212763	7.44E-06	2.25E-27	mr1120	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
vg0818212763	2.59E-09	1.22E-33	mr1123	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
vg0818212763	NA	1.02E-06	mr1126	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
vg0818212763	NA	6.51E-06	mr1184	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
vg0818212763	3.45E-06	3.20E-23	mr1240	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
vg0818212763	8.98E-08	2.17E-23	mr1242	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
vg0818212763	7.97E-07	1.77E-28	mr1247	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
vg0818212763	NA	3.18E-08	mr1369	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
vg0818212763	NA	5.44E-06	mr1445	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
vg0818212763	NA	2.01E-08	mr1453	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
vg0818212763	3.24E-07	8.44E-19	mr1496	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
vg0818212763	NA	7.07E-06	mr1545	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
vg0818212763	NA	1.72E-26	mr1589	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
vg0818212763	NA	4.01E-08	mr1652	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
vg0818212763	NA	9.45E-08	mr1706	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
vg0818212763	NA	3.89E-10	mr1730	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
vg0818212763	NA	8.27E-07	mr1762	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
vg0818212763	NA	1.94E-33	mr1858	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
vg0818212763	NA	1.73E-33	mr1859	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
vg0818212763	NA	1.50E-31	mr1868	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
vg0818212763	NA	7.55E-06	mr1906	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
vg0818212763	NA	2.35E-19	mr1911	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
vg0818212763	6.26E-07	2.68E-27	mr1917	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
vg0818212763	NA	1.69E-13	mr1918	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
vg0818212763	NA	1.85E-22	mr1936	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
vg0818212763	NA	1.33E-09	mr1939	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
vg0818212763	NA	3.29E-22	mr1961	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
vg0818212763	NA	5.08E-23	mr1095_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
vg0818212763	NA	1.41E-37	mr1098_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
vg0818212763	NA	5.46E-29	mr1099_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
vg0818212763	3.76E-08	3.97E-24	mr1113_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
vg0818212763	1.70E-08	1.42E-22	mr1114_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
vg0818212763	1.12E-08	4.33E-26	mr1117_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
vg0818212763	2.69E-06	NA	mr1118_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
vg0818212763	2.66E-08	3.93E-23	mr1119_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
vg0818212763	1.68E-08	1.78E-31	mr1120_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
vg0818212763	4.29E-09	4.00E-30	mr1123_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
vg0818212763	2.55E-07	4.85E-24	mr1240_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
vg0818212763	9.82E-08	NA	mr1242_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
vg0818212763	8.50E-09	5.36E-31	mr1247_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
vg0818212763	NA	4.73E-09	mr1388_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
vg0818212763	7.58E-06	NA	mr1495_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
vg0818212763	1.96E-07	5.61E-16	mr1496_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
vg0818212763	NA	1.98E-15	mr1587_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
vg0818212763	NA	8.60E-17	mr1911_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
vg0818212763	NA	4.11E-12	mr1918_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
vg0818212763	NA	3.07E-06	mr1929_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
vg0818212763	NA	5.76E-19	mr1936_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
vg0818212763	7.53E-06	3.86E-21	mr1961_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