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Detailed information for vg0820717502:

Variant ID: vg0820717502 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 20717502
Reference Allele: GGATTAlternative Allele: AGATT,G
Primary Allele: GGATTSecondary Allele: AGATT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTCATTTTGTTCTATACCCGACTGGTTTCCAGTCGGGGGCTCCTGATCAGCACCTATCTCAGCTTCGGCCGACTGGTTTCCAGTCGGAGGCTCGTTGCT[GGATT/AGATT,G]
GTACATTGTCGGTTGCTGGTTGATTATTACTCGGGCGATCTTCGGCAGTTGGCCCGGTTTCAGTTGTAGGACCAGTCTCCGTGCTGGTCGTTTCAGAGTT

Reverse complement sequence

AACTCTGAAACGACCAGCACGGAGACTGGTCCTACAACTGAAACCGGGCCAACTGCCGAAGATCGCCCGAGTAATAATCAACCAGCAACCGACAATGTAC[AATCC/AATCT,C]
AGCAACGAGCCTCCGACTGGAAACCAGTCGGCCGAAGCTGAGATAGGTGCTGATCAGGAGCCCCCGACTGGAAACCAGTCGGGTATAGAACAAAATGAAG

Allele Frequencies:

Populations Population SizeFrequency of GGATT(primary allele) Frequency of AGATT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.30% 3.30% 0.38% 0.00% NA
All Indica  2759 97.50% 2.50% 0.04% 0.00% NA
All Japonica  1512 93.80% 5.00% 1.12% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 94.30% 5.70% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.00% 0.13% 0.00% NA
Temperate Japonica  767 89.00% 8.70% 2.22% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0820717502 GGATT -> G LOC_Os08g33250.1 frameshift_variant ; p.Gln424fs; HIGH N Average:51.481; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N
vg0820717502 GGATT -> G LOC_Os08g33240.1 upstream_gene_variant ; 2260.0bp to feature; MODIFIER N Average:51.481; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N
vg0820717502 GGATT -> G LOC_Os08g33260.1 upstream_gene_variant ; 2902.0bp to feature; MODIFIER N Average:51.481; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N
vg0820717502 GGATT -> G LOC_Os08g33220.1 downstream_gene_variant ; 4931.0bp to feature; MODIFIER N Average:51.481; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N
vg0820717502 GGATT -> AGATT LOC_Os08g33250.1 synonymous_variant ; p.Ser425Ser; LOW synonymous_codon Average:51.481; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820717502 NA 2.09E-06 mr1677 Jap_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
vg0820717502 3.13E-06 3.13E-06 mr1950 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