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Detailed information for vg1123001258:

Variant ID: vg1123001258 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 23001258
Reference Allele: AAlternative Allele: AGGATCGAATTACAAGAACTAAG,T,AGGATCGAATCACAAGAACTAAG,G
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTCATTATCCAAAAAATCCTCACTGTTCAAACACTGCCACTTGGTTGTGTGAACCTTTTGTAAGGAGTGAGTCTATGTACTCTAGTTTGGGTTTTAGAG[A/AGGATCGAATTACAAGAACTAAG,T,AGGATCGAATCACAAGAACTAAG,G]
CCAGGTTTAAATCCATTTTCCATTTTCATAAAAATCGAGCGATGAATACACCATTACCCTGGTCGCTTTCTCATGCATCCAGGCATGCATCACCAGCGTT

Reverse complement sequence

AACGCTGGTGATGCATGCCTGGATGCATGAGAAAGCGACCAGGGTAATGGTGTATTCATCGCTCGATTTTTATGAAAATGGAAAATGGATTTAAACCTGG[T/CTTAGTTCTTGTAATTCGATCCT,A,CTTAGTTCTTGTGATTCGATCCT,C]
CTCTAAAACCCAAACTAGAGTACATAGACTCACTCCTTACAAAAGGTTCACACAACCAAGTGGCAGTGTTTGAACAGTGAGGATTTTTTGGATAATGAAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.90% 3.20% 21.69% 18.81% AGGATCGAATCACAAGAACTAAG: 2.22%; AGGATCGAATTACAAGAACTAAG: 0.17%; G: 0.02%
All Indica  2759 40.40% 4.30% 24.14% 27.69% AGGATCGAATCACAAGAACTAAG: 3.12%; AGGATCGAATTACAAGAACTAAG: 0.29%; G: 0.04%
All Japonica  1512 85.60% 0.90% 9.39% 3.64% AGGATCGAATCACAAGAACTAAG: 0.53%
Aus  269 2.60% 7.10% 69.89% 17.10% AGGATCGAATCACAAGAACTAAG: 3.35%
Indica I  595 81.50% 1.30% 7.23% 8.40% AGGATCGAATCACAAGAACTAAG: 1.51%
Indica II  465 5.60% 5.20% 35.27% 47.74% AGGATCGAATCACAAGAACTAAG: 6.02%; AGGATCGAATTACAAGAACTAAG: 0.22%
Indica III  913 36.50% 5.60% 28.48% 26.62% AGGATCGAATCACAAGAACTAAG: 2.52%; AGGATCGAATTACAAGAACTAAG: 0.33%
Indica Intermediate  786 34.60% 4.50% 25.32% 31.68% AGGATCGAATCACAAGAACTAAG: 3.31%; AGGATCGAATTACAAGAACTAAG: 0.51%; G: 0.13%
Temperate Japonica  767 91.10% 0.30% 4.69% 3.65% AGGATCGAATCACAAGAACTAAG: 0.26%
Tropical Japonica  504 81.20% 0.60% 14.48% 2.78% AGGATCGAATCACAAGAACTAAG: 0.99%
Japonica Intermediate  241 77.20% 3.30% 13.69% 5.39% AGGATCGAATCACAAGAACTAAG: 0.41%
VI/Aromatic  96 90.60% 1.00% 6.25% 2.08% NA
Intermediate  90 46.70% 1.10% 25.56% 24.44% AGGATCGAATCACAAGAACTAAG: 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
vg1123001258 A -> AGGATCGAATTACAAGAACTAAG LOC_Os11g38720-LOC_Os11g38750 intergenic_region ; MODIFIER silent_mutation Average:54.637; most accessible tissue: Callus, score: 78.946 N N N N
vg1123001258 A -> T LOC_Os11g38720-LOC_Os11g38750 intergenic_region ; MODIFIER silent_mutation Average:54.637; most accessible tissue: Callus, score: 78.946 N N N N
vg1123001258 A -> AGGATCGAATCACAAGAACTAAG LOC_Os11g38720-LOC_Os11g38750 intergenic_region ; MODIFIER silent_mutation Average:54.637; most accessible tissue: Callus, score: 78.946 N N N N
vg1123001258 A -> DEL N N silent_mutation Average:54.637; most accessible tissue: Callus, score: 78.946 N N N N
vg1123001258 A -> G LOC_Os11g38720-LOC_Os11g38750 intergenic_region ; MODIFIER silent_mutation Average:54.637; most accessible tissue: Callus, score: 78.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123001258 NA 1.82E-06 mr1074 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
vg1123001258 NA 5.05E-06 mr1130 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
vg1123001258 NA 1.22E-07 mr1272 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
vg1123001258 NA 3.52E-06 mr1542 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
vg1123001258 NA 5.20E-11 mr1659 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
vg1123001258 NA 6.66E-10 mr1935 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
vg1123001258 NA 1.39E-06 mr1942 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
vg1123001258 NA 8.34E-06 mr1050_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
vg1123001258 NA 7.95E-06 mr1169_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
vg1123001258 NA 2.57E-09 mr1565_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
vg1123001258 NA 3.48E-10 mr1715_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
vg1123001258 NA 1.43E-06 mr1842_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
vg1123001258 NA 5.44E-09 mr1902_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
vg1123001258 NA 2.11E-06 mr1923_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
vg1123001258 NA 1.03E-08 mr1933_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
vg1123001258 NA 8.18E-08 mr1942_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