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Detailed information for vg1122800334:

Variant ID: vg1122800334 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22800334
Reference Allele: TAlternative Allele: G,C
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATGGGTTGCAGAAGGTTTGACACTCAAGGAAGATTGGTCCAGTTCTGTGCATCAGGCAAAGATTTGATGCCCTCATCCATCGGTATCTTGTTTGTCCTG[T/G,C]
TGATATTGGTGGCACAGGAAAGGTGAAGAGCTGTGTGGTAAATGATCCAGTTCATGGGTTCATTACCACAATTGCCAGAAAACAACATATTGTGGAGACA

Reverse complement sequence

TGTCTCCACAATATGTTGTTTTCTGGCAATTGTGGTAATGAACCCATGAACTGGATCATTTACCACACAGCTCTTCACCTTTCCTGTGCCACCAATATCA[A/C,G]
CAGGACAAACAAGATACCGATGGATGAGGGCATCAAATCTTTGCCTGATGCACAGAACTGGACCAATCTTCCTTGAGTGTCAAACCTTCTGCAACCCATT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.50% 24.60% 3.07% 13.25% C: 1.54%
All Indica  2759 50.70% 34.70% 2.28% 11.24% C: 1.16%
All Japonica  1512 74.80% 11.00% 2.51% 9.85% C: 1.85%
Aus  269 26.00% 9.70% 8.92% 51.67% C: 3.72%
Indica I  595 18.20% 77.00% 0.84% 4.03% NA
Indica II  465 91.60% 4.70% 1.72% 0.86% C: 1.08%
Indica III  913 41.90% 28.10% 4.05% 24.32% C: 1.53%
Indica Intermediate  786 61.20% 27.90% 1.65% 7.63% C: 1.65%
Temperate Japonica  767 71.60% 11.00% 1.17% 16.17% C: 0.13%
Tropical Japonica  504 79.60% 7.70% 4.37% 3.77% C: 4.56%
Japonica Intermediate  241 75.10% 17.80% 2.90% 2.49% C: 1.66%
VI/Aromatic  96 56.20% 7.30% 13.54% 22.92% NA
Intermediate  90 72.20% 10.00% 7.78% 6.67% C: 3.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1122800334 T -> DEL N N silent_mutation Average:55.829; most accessible tissue: Minghui63 flag leaf, score: 84.608 N N N N
vg1122800334 T -> G LOC_Os11g38480.1 5_prime_UTR_variant ; 296.0bp to feature; MODIFIER silent_mutation Average:55.829; most accessible tissue: Minghui63 flag leaf, score: 84.608 N N N N
vg1122800334 T -> G LOC_Os11g38470.1 upstream_gene_variant ; 4672.0bp to feature; MODIFIER silent_mutation Average:55.829; most accessible tissue: Minghui63 flag leaf, score: 84.608 N N N N
vg1122800334 T -> C LOC_Os11g38480.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:55.829; most accessible tissue: Minghui63 flag leaf, score: 84.608 N N N N
vg1122800334 T -> C LOC_Os11g38480.1 5_prime_UTR_variant ; 296.0bp to feature; MODIFIER silent_mutation Average:55.829; most accessible tissue: Minghui63 flag leaf, score: 84.608 N N N N
vg1122800334 T -> C LOC_Os11g38470.1 upstream_gene_variant ; 4672.0bp to feature; MODIFIER silent_mutation Average:55.829; most accessible tissue: Minghui63 flag leaf, score: 84.608 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122800334 NA 7.34E-06 mr1074 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
vg1122800334 1.61E-06 NA mr1378 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
vg1122800334 NA 2.14E-06 mr1378 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
vg1122800334 NA 1.51E-08 mr1677 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
vg1122800334 NA 3.08E-07 mr1805_2 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