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Detailed information for vg1218054771:

Variant ID: vg1218054771 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 18054771
Reference Allele: GGACTTAACTTTA	Alternative Allele: AGACTTAACTTTA,TGACTTAACTTTA,G
Primary Allele: GGACTTAACTTTA	Secondary Allele: AGACTTAACTTTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAAGAAAAAAAGTTATGTTGCACTTTGATTTCGGATTGAGTCATTAGTTTGAAAAACGCTTGGAGTTTTCAAAGGGTATAAGGTGGTGCTTGGATCCAG[GGACTTAACTTTA/AGACTTAACTTTA,TGACTTAACTTTA,G]
GTCCCTATATTTAGACACTAATTTAGAGTATTAGATATAGACTACTTACAAAACTAATTACATAAATGAAAACTAATTCGCGAGACAAATATTTTAAGCC

Reverse complement sequence

GGCTTAAAATATTTGTCTCGCGAATTAGTTTTCATTTATGTAATTAGTTTTGTAAGTAGTCTATATCTAATACTCTAAATTAGTGTCTAAATATAGGGAC[TAAAGTTAAGTCC/TAAAGTTAAGTCT,TAAAGTTAAGTCA,C]
CTGGATCCAAGCACCACCTTATACCCTTTGAAAACTCCAAGCGTTTTTCAAACTAATGACTCAATCCGAAATCAAAGTGCAACATAACTTTTTTTCTTCG

Allele Frequencies:

Populations	Population Size	Frequency of GGACTTAACTTTA(primary allele)	Frequency of AGACTTAACTTTA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.30%	18.50%	0.11%	0.47%	TGACTTAACTTTA: 0.59%; G: 0.04%
All Indica	2759	96.30%	2.00%	0.04%	0.80%	TGACTTAACTTTA: 0.83%; G: 0.07%
All Japonica	1512	50.30%	49.20%	0.13%	0.00%	TGACTTAACTTTA: 0.33%
Aus	269	90.30%	9.70%	0.00%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	98.90%	0.60%	0.00%	0.43%	NA
Indica III	913	95.80%	0.40%	0.11%	2.08%	TGACTTAACTTTA: 1.31%; G: 0.22%
Indica Intermediate	786	93.80%	4.70%	0.00%	0.13%	TGACTTAACTTTA: 1.40%
Temperate Japonica	767	65.60%	34.30%	0.13%	0.00%	NA
Tropical Japonica	504	26.80%	72.80%	0.20%	0.00%	TGACTTAACTTTA: 0.20%
Japonica Intermediate	241	51.00%	47.30%	0.00%	0.00%	TGACTTAACTTTA: 1.66%
VI/Aromatic	96	68.80%	30.20%	1.04%	0.00%	NA
Intermediate	90	77.80%	21.10%	1.11%	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
vg1218054771	GGACTTAACTTTA -> TGACTTAACTTTA	LOC_Os12g30120-LOC_Os12g30130	intergenic_region ; MODIFIER	silent_mutation	Average:47.411; most accessible tissue: Callus, score: 75.511	N	N	N	N
vg1218054771	GGACTTAACTTTA -> DEL	N	N	silent_mutation	Average:47.411; most accessible tissue: Callus, score: 75.511	N	N	N	N
vg1218054771	GGACTTAACTTTA -> G	LOC_Os12g30120-LOC_Os12g30130	intergenic_region ; MODIFIER	silent_mutation	Average:47.411; most accessible tissue: Callus, score: 75.511	N	N	N	N
vg1218054771	GGACTTAACTTTA -> AGACTTAACTTTA	LOC_Os12g30120-LOC_Os12g30130	intergenic_region ; MODIFIER	silent_mutation	Average:47.411; most accessible tissue: Callus, score: 75.511	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218054771	NA	7.89E-07	mr1010	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
vg1218054771	NA	3.18E-06	mr1041	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
vg1218054771	4.52E-06	NA	mr1046	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
vg1218054771	8.17E-06	NA	mr1048	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
vg1218054771	3.09E-06	NA	mr1060	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
vg1218054771	NA	2.14E-10	mr1070	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
vg1218054771	NA	1.92E-13	mr1084	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
vg1218054771	NA	1.16E-09	mr1097	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
vg1218054771	NA	1.19E-08	mr1163	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
vg1218054771	NA	2.85E-06	mr1171	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
vg1218054771	NA	4.35E-06	mr1171	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
vg1218054771	NA	7.55E-06	mr1192	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
vg1218054771	NA	1.13E-15	mr1205	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
vg1218054771	1.10E-06	4.18E-09	mr1206	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
vg1218054771	NA	9.30E-06	mr1215	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
vg1218054771	NA	4.51E-07	mr1245	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
vg1218054771	NA	4.98E-07	mr1278	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
vg1218054771	NA	8.73E-06	mr1280	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
vg1218054771	NA	7.60E-06	mr1284	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
vg1218054771	NA	2.07E-06	mr1293	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
vg1218054771	NA	3.76E-10	mr1302	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
vg1218054771	NA	1.10E-08	mr1315	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
vg1218054771	NA	9.06E-06	mr1319	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
vg1218054771	NA	6.90E-07	mr1338	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
vg1218054771	7.06E-06	7.08E-06	mr1356	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
vg1218054771	6.34E-06	NA	mr1359	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
vg1218054771	NA	8.83E-06	mr1359	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
vg1218054771	NA	3.42E-07	mr1392	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
vg1218054771	NA	1.45E-07	mr1405	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
vg1218054771	8.06E-06	1.82E-09	mr1418	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
vg1218054771	NA	2.83E-09	mr1420	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
vg1218054771	NA	4.80E-06	mr1450	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
vg1218054771	NA	8.74E-07	mr1461	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
vg1218054771	5.35E-06	2.35E-11	mr1488	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
vg1218054771	NA	1.95E-07	mr1492	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
vg1218054771	NA	4.04E-06	mr1492	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
vg1218054771	NA	2.99E-11	mr1506	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
vg1218054771	5.66E-06	2.36E-08	mr1507	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
vg1218054771	NA	4.37E-06	mr1511	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
vg1218054771	NA	2.57E-14	mr1521	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
vg1218054771	NA	5.35E-07	mr1548	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
vg1218054771	NA	7.08E-09	mr1604	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
vg1218054771	NA	2.17E-08	mr1617	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
vg1218054771	NA	1.73E-11	mr1683	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
vg1218054771	NA	4.95E-06	mr1729	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
vg1218054771	NA	2.59E-08	mr1764	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
vg1218054771	NA	8.32E-06	mr1773	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
vg1218054771	NA	7.48E-14	mr1775	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
vg1218054771	1.17E-07	6.30E-13	mr1779	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
vg1218054771	2.82E-06	2.82E-06	mr1779	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
vg1218054771	NA	7.67E-06	mr1786	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
vg1218054771	NA	2.00E-10	mr1797	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
vg1218054771	NA	2.00E-10	mr1801	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
vg1218054771	NA	5.56E-07	mr1802	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
vg1218054771	NA	2.44E-06	mr1809	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
vg1218054771	7.36E-06	1.27E-10	mr1810	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
vg1218054771	NA	1.29E-06	mr1811	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
vg1218054771	NA	4.31E-07	mr1812	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
vg1218054771	NA	5.20E-06	mr1816	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
vg1218054771	6.70E-06	2.79E-10	mr1824	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
vg1218054771	NA	1.13E-06	mr1832	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
vg1218054771	NA	7.37E-07	mr1881	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
vg1218054771	NA	5.32E-08	mr1886	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
vg1218054771	8.08E-06	NA	mr1920	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
vg1218054771	NA	1.41E-08	mr1992	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