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Detailed information for vg0812252841:

Variant ID: vg0812252841 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 12252841
Reference Allele: ATTATGGAATTGATATGGTCTTCTGATGCGGAAATCCTAACGCGCGGGTGATCGCCCCCGCGCTGCCCTGGCGATCACCCCTCGCCTCCAlternative Allele: CTTATGGAATTGATATGGTCTTCTGATGCGGAAATCCTAACGCGCGGGTGATCGCCCCCGCGCTGCCCTGGCGATCACCCCTCGCCTCC,A
Primary Allele: ATTATGGAATTGATATGGTC TTCTGATGCGGAAATCCTAA CGCGCGGGTGATCGCCCCCG CGCTGCCCTGGCGATCACCC CTCGCCTCCSecondary Allele: CTTATGGAATTGATATGGTC TTCTGATGCGGAAATCCTAA CGCGCGGGTGATCGCCCCCG CGCTGCCCTGGCGATCACCC CTCGCCTCC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGATCTATCTACTTCGTTTTCACACCTAGGGTAACGAACTGTGGATACGTGGATTAGAGAATGTTAAGTATGGTCGGATATAATGGCTGCATGGCTCGC[ATTATGGAATTGATATGGTCTTCTGATGCGGAAATCCTAACGCGCGGGTGATCGCCCCCGCGCTGCCCTGGCGATCACCCCTCGCCTCC/CTTATGGAATTGATATGGTCTTCTGATGCGGAAATCCTAACGCGCGGGTGATCGCCCCCGCGCTGCCCTGGCGATCACCCCTCGCCTCC,A]
CCCTGTGCTCCTCTCTCTCTTCTCCCCCTTCCTCCTCCCCTTCTTCTCTTCCTATTACAGTACACCACAAAAAATTTTTAAAAAAACAAAAAGTTAAAAA

Reverse complement sequence

TTTTTAACTTTTTGTTTTTTTAAAAATTTTTTGTGGTGTACTGTAATAGGAAGAGAAGAAGGGGAGGAGGAAGGGGGAGAAGAGAGAGAGGAGCACAGGG[GGAGGCGAGGGGTGATCGCCAGGGCAGCGCGGGGGCGATCACCCGCGCGTTAGGATTTCCGCATCAGAAGACCATATCAATTCCATAAT/GGAGGCGAGGGGTGATCGCCAGGGCAGCGCGGGGGCGATCACCCGCGCGTTAGGATTTCCGCATCAGAAGACCATATCAATTCCATAAG,T]
GCGAGCCATGCAGCCATTATATCCGACCATACTTAACATTCTCTAATCCACGTATCCACAGTTCGTTACCCTAGGTGTGAAAACGAAGTAGATAGATCAA

Allele Frequencies:

Populations Population SizeFrequency of ATTATGGAATTGATATGGTC TTCTGATGCGGAAATCCTAA CGCGCGGGTGATCGCCCCCG CGCTGCCCTGGCGATCACCC CTCGCCTCC(primary allele) Frequency of CTTATGGAATTGATATGGTC TTCTGATGCGGAAATCCTAA CGCGCGGGTGATCGCCCCCG CGCTGCCCTGGCGATCACCC CTCGCCTCC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.00% 2.20% 0.80% 0.00% A: 0.08%
All Indica  2759 95.00% 3.70% 1.30% 0.00% A: 0.04%
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 98.10% 0.00% 0.74% 0.00% A: 1.12%
Indica I  595 90.30% 7.10% 2.69% 0.00% NA
Indica II  465 98.30% 1.30% 0.43% 0.00% NA
Indica III  913 99.30% 0.40% 0.22% 0.00% NA
Indica Intermediate  786 91.60% 6.20% 2.04% 0.00% A: 0.13%
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg0812252841 ATTATGGAATTGATATGGTCTTCTGATGCGGAAATCCTAACGCGCGGGTGATCGCCCCCGCGCTGCCCTGGCGATCACCCCTCGCCTCC -> A LOC_Os08g20400.1 downstream_gene_variant ; 3477.0bp to feature; MODIFIER silent_mutation Average:73.709; most accessible tissue: Zhenshan97 young leaf, score: 82.539 N N N N
vg0812252841 ATTATGGAATTGATATGGTCTTCTGATGCGGAAATCCTAACGCGCGGGTGATCGCCCCCGCGCTGCCCTGGCGATCACCCCTCGCCTCC -> A LOC_Os08g20410.1 downstream_gene_variant ; 4148.0bp to feature; MODIFIER silent_mutation Average:73.709; most accessible tissue: Zhenshan97 young leaf, score: 82.539 N N N N
vg0812252841 ATTATGGAATTGATATGGTCTTCTGATGCGGAAATCCTAACGCGCGGGTGATCGCCCCCGCGCTGCCCTGGCGATCACCCCTCGCCTCC -> A LOC_Os08g20400-LOC_Os08g20410 intergenic_region ; MODIFIER silent_mutation Average:73.709; most accessible tissue: Zhenshan97 young leaf, score: 82.539 N N N N
vg0812252841 ATTATGGAATTGATATGGTCTTCTGATGCGGAAATCCTAACGCGCGGGTGATCGCCCCCGCGCTGCCCTGGCGATCACCCCTCGCCTCC -> CTTATGGAATTGATATGGTCTTCTGATGCG GAAATCCTAACGCGCGGGTGATCGCCCCCG CGCTGCCCTGGCGATCACCCCTCGCCTCC LOC_Os08g20400.1 downstream_gene_variant ; 3476.0bp to feature; MODIFIER silent_mutation Average:73.709; most accessible tissue: Zhenshan97 young leaf, score: 82.539 N N N N
vg0812252841 ATTATGGAATTGATATGGTCTTCTGATGCGGAAATCCTAACGCGCGGGTGATCGCCCCCGCGCTGCCCTGGCGATCACCCCTCGCCTCC -> CTTATGGAATTGATATGGTCTTCTGATGCG GAAATCCTAACGCGCGGGTGATCGCCCCCG CGCTGCCCTGGCGATCACCCCTCGCCTCC LOC_Os08g20410.1 downstream_gene_variant ; 4149.0bp to feature; MODIFIER silent_mutation Average:73.709; most accessible tissue: Zhenshan97 young leaf, score: 82.539 N N N N
vg0812252841 ATTATGGAATTGATATGGTCTTCTGATGCGGAAATCCTAACGCGCGGGTGATCGCCCCCGCGCTGCCCTGGCGATCACCCCTCGCCTCC -> CTTATGGAATTGATATGGTCTTCTGATGCG GAAATCCTAACGCGCGGGTGATCGCCCCCG CGCTGCCCTGGCGATCACCCCTCGCCTCC LOC_Os08g20400-LOC_Os08g20410 intergenic_region ; MODIFIER silent_mutation Average:73.709; most accessible tissue: Zhenshan97 young leaf, score: 82.539 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0812252841 1.70E-06 NA mr1458 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
vg0812252841 NA 3.21E-08 mr1458 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