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Detailed information for vg0120798282:

Variant ID: vg0120798282 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 20798282
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGAGTGCCATTATCGGTGATGATCCGATTAGGTACCCCAAACCGATGCACAATGTTAATGAAAAAATCTCTAGCTTTATCTGCTGTGATCGTGATGACC[G/A]
GTTTAGCCTCAATCCACTTGGAGAATTTGTCGATAGCCACAAAGATATGCGTGTAACTGCCGACTGCCCTTTTAAACGGGCCGACCATATCAAGCCCCCA

Reverse complement sequence

TGGGGGCTTGATATGGTCGGCCCGTTTAAAAGGGCAGTCGGCAGTTACACGCATATCTTTGTGGCTATCGACAAATTCTCCAAGTGGATTGAGGCTAAAC[C/T]
GGTCATCACGATCACAGCAGATAAAGCTAGAGATTTTTTCATTAACATTGTGCATCGGTTTGGGGTACCTAATCGGATCATCACCGATAATGGCACTCAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.20% 0.08% 0.00% NA
All Indica  2759 99.50% 0.30% 0.14% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.50% 0.30% 0.17% 0.00% NA
Indica II  465 98.90% 0.90% 0.22% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.50% 0.40% 0.13% 0.00% NA
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
vg0120798282 G -> A LOC_Os01g37240.1 missense_variant ; p.Pro785Leu; MODERATE N Average:32.169; most accessible tissue: Minghui63 flag leaf, score: 72.028 N N N N
vg0120798282 G -> A LOC_Os01g37230.1 downstream_gene_variant ; 1075.0bp to feature; MODIFIER N Average:32.169; most accessible tissue: Minghui63 flag leaf, score: 72.028 N N N N
vg0120798282 G -> A LOC_Os01g37250.1 downstream_gene_variant ; 2744.0bp to feature; MODIFIER N Average:32.169; most accessible tissue: Minghui63 flag leaf, score: 72.028 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0120798282 5.68E-06 5.68E-06 mr1499 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
vg0120798282 3.79E-07 NA mr1735 Ind_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
vg0120798282 7.25E-07 8.29E-07 mr1818 Ind_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
vg0120798282 NA 6.79E-06 mr1914 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