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Detailed information for vg1205142686:

Variant ID: vg1205142686 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 5142686
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTGGCTGGATCACGTTGAGGGGTGGATAAAAATCTGACACAATCAATGCGTGCTGTATGGATTCTCAAATCCTTCCCTGTTTATGTGTTATGATGCTA[G/T]
GCATACTCCTGTTAATGCTTCCATATAATGACTGCAAGAGTATAATGTTTCCTTCAAATATAAGATAGCATATTGATAGGTTGGTATTCCGTTCTCCTTA

Reverse complement sequence

TAAGGAGAACGGAATACCAACCTATCAATATGCTATCTTATATTTGAAGGAAACATTATACTCTTGCAGTCATTATATGGAAGCATTAACAGGAGTATGC[C/A]
TAGCATCATAACACATAAACAGGGAAGGATTTGAGAATCCATACAGCACGCATTGATTGTGTCAGATTTTTATCCACCCCTCAACGTGATCCAGCCAAAT

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 24.70% 12.20% 7.85% 55.23% NA
All Indica  2759 3.80% 1.00% 5.00% 90.21% NA
All Japonica  1512 54.60% 35.20% 8.80% 1.39% NA
Aus  269 40.50% 0.40% 32.34% 26.77% NA
Indica I  595 2.90% 0.70% 5.55% 90.92% NA
Indica II  465 2.20% 1.90% 4.30% 91.61% NA
Indica III  913 2.80% 0.70% 3.29% 93.21% NA
Indica Intermediate  786 6.50% 1.10% 7.00% 85.37% NA
Temperate Japonica  767 30.20% 57.20% 11.60% 0.91% NA
Tropical Japonica  504 89.50% 3.40% 4.56% 2.58% NA
Japonica Intermediate  241 59.30% 31.50% 8.71% 0.41% NA
VI/Aromatic  96 94.80% 0.00% 4.17% 1.04% NA
Intermediate  90 43.30% 16.70% 10.00% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1205142686 G -> DEL N N silent_mutation Average:11.275; most accessible tissue: Callus, score: 64.811 N N N N
vg1205142686 G -> T LOC_Os12g09739.1 intron_variant ; MODIFIER silent_mutation Average:11.275; most accessible tissue: Callus, score: 64.811 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1205142686 6.55E-08 NA mr1354 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
vg1205142686 1.18E-06 NA mr1354 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
vg1205142686 NA 1.53E-10 mr1712 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
vg1205142686 NA 3.98E-06 mr1955 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
vg1205142686 NA 9.33E-07 mr1977_2 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