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Detailed information for vg0326972463:

Variant ID: vg0326972463 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 26972463
Reference Allele: TTTATTGTTTG	Alternative Allele: TTATTGTGCATCATTGAATTATTGTTTG,ATTATTGTTTG,T
Primary Allele: TTATTGTGCATCATTGAATT ATTGTTTG	Secondary Allele: TTTATTGTTTG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTATAAATATATTGATTGCTATTCTATTATGGATCTTAAATGATTTTTTGATCGTTTCCTTGTTATTTATTTATTAAGTCACATCCATGTGCATCATTGA[TTTATTGTTTG/TTATTGTGCATCATTGAATTATTGTTTG,ATTATTGTTTG,T]
TTAGACTAAACCTGGTGAGGAGTGGGATCATTTAGTTTTGGTTAAATTATAGTGTAGATTAGTCGTCACGAAGCGAGGTACACATGTGCACAGTAGAAAT

Reverse complement sequence

ATTTCTACTGTGCACATGTGTACCTCGCTTCGTGACGACTAATCTACACTATAATTTAACCAAAACTAAATGATCCCACTCCTCACCAGGTTTAGTCTAA[CAAACAATAAA/CAAACAATAATTCAATGATGCACAATAA,CAAACAATAAT,A]
TCAATGATGCACATGGATGTGACTTAATAAATAAATAACAAGGAAACGATCAAAAAATCATTTAAGATCCATAATAGAATAGCAATCAATATATTTATAG

Allele Frequencies:

Populations	Population Size	Frequency of TTATTGTGCATCATTGAATT ATTGTTTG(primary allele)	Frequency of TTTATTGTTTG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.80%	35.10%	1.44%	0.11%	ATTATTGTTTG: 7.49%; T: 0.04%
All Indica	2759	83.80%	1.30%	2.36%	0.11%	ATTATTGTTTG: 12.47%
All Japonica	1512	1.20%	98.70%	0.00%	0.07%	ATTATTGTTTG: 0.07%
Aus	269	95.50%	3.30%	0.00%	0.00%	ATTATTGTTTG: 1.12%
Indica I	595	87.40%	1.00%	5.55%	0.17%	ATTATTGTTTG: 5.88%
Indica II	465	80.60%	1.50%	2.15%	0.00%	ATTATTGTTTG: 15.70%
Indica III	913	85.30%	0.90%	0.55%	0.11%	ATTATTGTTTG: 13.14%
Indica Intermediate	786	81.00%	1.90%	2.16%	0.13%	ATTATTGTTTG: 14.76%
Temperate Japonica	767	0.70%	99.30%	0.00%	0.00%	NA
Tropical Japonica	504	1.60%	98.00%	0.00%	0.20%	ATTATTGTTTG: 0.20%
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	85.40%	1.04%	0.00%	NA
Intermediate	90	43.30%	44.40%	2.22%	1.11%	ATTATTGTTTG: 6.67%; T: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0326972463	TTTATTGTTTG -> T	LOC_Os03g47620.1	downstream_gene_variant ; 2245.0bp to feature; MODIFIER	silent_mutation	Average:49.733; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0326972463	TTTATTGTTTG -> T	LOC_Os03g47629.1	downstream_gene_variant ; 434.0bp to feature; MODIFIER	silent_mutation	Average:49.733; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0326972463	TTTATTGTTTG -> T	LOC_Os03g47629-LOC_Os03g47640	intergenic_region ; MODIFIER	silent_mutation	Average:49.733; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0326972463	TTTATTGTTTG -> DEL	N	N	silent_mutation	Average:49.733; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0326972463	TTTATTGTTTG -> TTATTGTGCATCATTGAATTATTGTTTG	LOC_Os03g47620.1	downstream_gene_variant ; 2246.0bp to feature; MODIFIER	silent_mutation	Average:49.733; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0326972463	TTTATTGTTTG -> TTATTGTGCATCATTGAATTATTGTTTG	LOC_Os03g47629.1	downstream_gene_variant ; 435.0bp to feature; MODIFIER	silent_mutation	Average:49.733; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0326972463	TTTATTGTTTG -> TTATTGTGCATCATTGAATTATTGTTTG	LOC_Os03g47629-LOC_Os03g47640	intergenic_region ; MODIFIER	silent_mutation	Average:49.733; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0326972463	TTTATTGTTTG -> ATTATTGTTTG	LOC_Os03g47620.1	downstream_gene_variant ; 2244.0bp to feature; MODIFIER	silent_mutation	Average:49.733; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0326972463	TTTATTGTTTG -> ATTATTGTTTG	LOC_Os03g47629.1	downstream_gene_variant ; 433.0bp to feature; MODIFIER	silent_mutation	Average:49.733; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0326972463	TTTATTGTTTG -> ATTATTGTTTG	LOC_Os03g47629-LOC_Os03g47640	intergenic_region ; MODIFIER	silent_mutation	Average:49.733; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0326972463	NA	6.45E-11	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
vg0326972463	4.12E-06	4.12E-06	mr1197	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
vg0326972463	NA	3.10E-12	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
vg0326972463	NA	6.21E-09	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
vg0326972463	NA	1.32E-06	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
vg0326972463	NA	4.04E-16	mr1376	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
vg0326972463	NA	3.32E-12	mr1386	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
vg0326972463	NA	9.21E-29	mr1414	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
vg0326972463	NA	4.04E-16	mr1431	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
vg0326972463	NA	1.59E-08	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
vg0326972463	NA	1.75E-06	mr1508	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
vg0326972463	NA	7.05E-08	mr1514	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
vg0326972463	NA	1.12E-24	mr1571	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
vg0326972463	NA	6.47E-12	mr1579	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
vg0326972463	NA	2.08E-06	mr1622	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
vg0326972463	NA	2.62E-07	mr1680	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
vg0326972463	NA	6.31E-14	mr1701	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
vg0326972463	NA	5.86E-28	mr1723	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
vg0326972463	NA	8.59E-12	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
vg0326972463	NA	4.12E-09	mr1776	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
vg0326972463	NA	2.95E-07	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
vg0326972463	NA	6.24E-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
vg0326972463	NA	5.33E-11	mr1846	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
vg0326972463	NA	4.67E-07	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
vg0326972463	NA	7.51E-07	mr1979	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