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Detailed information for vg0308082029:

Variant ID: vg0308082029 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 8082029
Reference Allele: TAAlternative Allele: AA,TAAA,TAA,TAAAA,TAAAAA,T
Primary Allele: AASecondary Allele: TA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTAAACCAGGATGAGGACATAAATGATATTTCTTTTTCCGGGTTAACACCGTTAGGTTACCTTTACAAAACAGGCAAGACCTGATTTTCATTTTTTTTT[TA/AA,TAAA,TAA,TAAAA,TAAAAA,T]
AAAAAAAGAGTGTCAAATGAGTAAACTTGGAAAAACAAGATAAAATCATTAGTTAGACTTCAAAACAGAGTAAAAATACAATTACCCTTAAATAATATTT

Reverse complement sequence

AAATATTATTTAAGGGTAATTGTATTTTTACTCTGTTTTGAAGTCTAACTAATGATTTTATCTTGTTTTTCCAAGTTTACTCATTTGACACTCTTTTTTT[TA/TT,TTTA,TTA,TTTTA,TTTTTA,A]
AAAAAAAAATGAAAATCAGGTCTTGCCTGTTTTGTAAAGGTAACCTAACGGTGTTAACCCGGAAAAAGAAATATCATTTATGTCCTCATCCTGGTTTACC

Allele Frequencies:

Populations Population SizeFrequency of AA(primary allele) Frequency of TA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.50% 32.10% 3.24% 0.00% TAA: 9.27%; TAAAA: 0.38%; TAAA: 0.34%; TAAAAA: 0.06%; T: 0.04%
All Indica  2759 76.30% 5.10% 3.55% 0.00% TAA: 13.88%; TAAAA: 0.62%; TAAA: 0.47%; TAAAAA: 0.04%; T: 0.04%
All Japonica  1512 10.40% 84.10% 2.51% 0.00% TAA: 2.65%; TAAAAA: 0.13%; TAAAA: 0.07%; T: 0.07%; TAAA: 0.07%
Aus  269 84.80% 9.30% 2.97% 0.00% TAA: 2.60%; TAAA: 0.37%
Indica I  595 79.70% 12.30% 5.71% 0.00% TAA: 2.02%; TAAAA: 0.34%
Indica II  465 93.80% 0.60% 1.29% 0.00% TAA: 3.66%; TAAAA: 0.43%; TAAA: 0.22%
Indica III  913 68.60% 3.60% 1.64% 0.00% TAA: 24.53%; TAAAA: 0.99%; TAAA: 0.44%; TAAAAA: 0.11%; T: 0.11%
Indica Intermediate  786 72.30% 4.20% 5.47% 0.00% TAA: 16.54%; TAAA: 1.02%; TAAAA: 0.51%
Temperate Japonica  767 5.60% 85.80% 3.39% 0.00% TAA: 4.95%; TAAAAA: 0.13%; TAAAA: 0.13%
Tropical Japonica  504 19.60% 78.20% 1.59% 0.00% T: 0.20%; TAAA: 0.20%; TAA: 0.20%
Japonica Intermediate  241 6.20% 91.30% 1.66% 0.00% TAAAAA: 0.41%; TAA: 0.41%
VI/Aromatic  96 52.10% 41.70% 4.17% 0.00% TAA: 2.08%
Intermediate  90 42.20% 44.40% 5.56% 0.00% TAA: 6.67%; TAAA: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0308082029 TA -> T LOC_Os03g14820-LOC_Os03g14840 intergenic_region ; MODIFIER silent_mutation Average:35.65; most accessible tissue: Zhenshan97 flower, score: 78.317 N N N N
vg0308082029 TA -> TAAAAA LOC_Os03g14820-LOC_Os03g14840 intergenic_region ; MODIFIER silent_mutation Average:35.65; most accessible tissue: Zhenshan97 flower, score: 78.317 N N N N
vg0308082029 TA -> TAAAA LOC_Os03g14820-LOC_Os03g14840 intergenic_region ; MODIFIER silent_mutation Average:35.65; most accessible tissue: Zhenshan97 flower, score: 78.317 N N N N
vg0308082029 TA -> TAA LOC_Os03g14820-LOC_Os03g14840 intergenic_region ; MODIFIER silent_mutation Average:35.65; most accessible tissue: Zhenshan97 flower, score: 78.317 N N N N
vg0308082029 TA -> TAAA LOC_Os03g14820-LOC_Os03g14840 intergenic_region ; MODIFIER silent_mutation Average:35.65; most accessible tissue: Zhenshan97 flower, score: 78.317 N N N N
vg0308082029 TA -> AA LOC_Os03g14820-LOC_Os03g14840 intergenic_region ; MODIFIER silent_mutation Average:35.65; most accessible tissue: Zhenshan97 flower, score: 78.317 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308082029 NA 4.89E-13 mr1169 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
vg0308082029 3.23E-06 3.14E-07 mr1695_2 Jap_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