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Detailed information for vg1003006014:

Variant ID: vg1003006014 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 3006014
Reference Allele: TAAlternative Allele: AA,T
Primary Allele: AASecondary Allele: TA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCAGTACTATCACCCACATGTATGGATCTACTCCTAGCAAATGGTTTTGAAGTTTTTTTTACGCAATCCATGCGTGTCTGCCGAAGGAAGATGAGTTC[TA/AA,T]
GCCATTAATCGATCCCTCAAGGGAATGATATGTGTATTTTCTTTCTCAAATGTAATGCAAACTGTTACGATATTTTTTTACAAAACTAGAAAGGTAGCCC

Reverse complement sequence

GGGCTACCTTTCTAGTTTTGTAAAAAAATATCGTAACAGTTTGCATTACATTTGAGAAAGAAAATACACATATCATTCCCTTGAGGGATCGATTAATGGC[TA/TT,A]
GAACTCATCTTCCTTCGGCAGACACGCATGGATTGCGTAAAAAAAACTTCAAAACCATTTGCTAGGAGTAGATCCATACATGTGGGTGATAGTACTGAGG

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 51.20% 29.50% 0.23% 0.00% T: 19.04%
All Indica  2759 84.80% 3.70% 0.22% 0.00% T: 11.31%
All Japonica  1512 1.60% 76.00% 0.20% 0.00% T: 22.22%
Aus  269 2.60% 14.10% 0.37% 0.00% T: 82.90%
Indica I  595 97.50% 0.50% 0.17% 0.00% T: 1.85%
Indica II  465 69.50% 1.70% 0.22% 0.00% T: 28.60%
Indica III  913 84.00% 6.70% 0.00% 0.00% T: 9.31%
Indica Intermediate  786 85.10% 3.80% 0.51% 0.00% T: 10.56%
Temperate Japonica  767 0.70% 63.20% 0.26% 0.00% T: 35.85%
Tropical Japonica  504 2.60% 94.20% 0.00% 0.00% T: 3.17%
Japonica Intermediate  241 2.50% 78.40% 0.41% 0.00% T: 18.67%
VI/Aromatic  96 25.00% 66.70% 0.00% 0.00% T: 8.33%
Intermediate  90 30.00% 45.60% 1.11% 0.00% T: 23.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1003006014 TA -> AA LOC_Os10g05950.1 upstream_gene_variant ; 4760.0bp to feature; MODIFIER silent_mutation Average:53.143; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg1003006014 TA -> AA LOC_Os10g05960.1 upstream_gene_variant ; 1827.0bp to feature; MODIFIER silent_mutation Average:53.143; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg1003006014 TA -> AA LOC_Os10g05960-LOC_Os10g05970 intergenic_region ; MODIFIER silent_mutation Average:53.143; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg1003006014 TA -> T LOC_Os10g05950.1 upstream_gene_variant ; 4761.0bp to feature; MODIFIER silent_mutation Average:53.143; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg1003006014 TA -> T LOC_Os10g05960.1 upstream_gene_variant ; 1828.0bp to feature; MODIFIER silent_mutation Average:53.143; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg1003006014 TA -> T LOC_Os10g05960-LOC_Os10g05970 intergenic_region ; MODIFIER silent_mutation Average:53.143; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003006014 NA 1.04E-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
vg1003006014 NA 7.97E-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
vg1003006014 NA 9.28E-11 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
vg1003006014 NA 4.64E-07 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
vg1003006014 3.62E-06 NA mr1962_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