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Detailed information for vg0802790437:

Variant ID: vg0802790437 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 2790437
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAGCATTCTATATAGTTCTTGCAGAAAACTGAATACTTCCCTTTTCTTATAACAGGTGATGCTGTCATACCAAACACACTTGGCTTATGTTCTGATTTG[T/C]
AATAGAACTCCTGAGATTGTGATAAGTTATAACTTATGACAAACACAAAAAAGAAAAACCTGAATGCAAATATTCATGGTAGTGTCAAAACAAAAAAAAA

Reverse complement sequence

TTTTTTTTTGTTTTGACACTACCATGAATATTTGCATTCAGGTTTTTCTTTTTTGTGTTTGTCATAAGTTATAACTTATCACAATCTCAGGAGTTCTATT[A/G]
CAAATCAGAACATAAGCCAAGTGTGTTTGGTATGACAGCATCACCTGTTATAAGAAAAGGGAAGTATTCAGTTTTCTGCAAGAACTATATAGAATGCTTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 2.80% 2.18% 0.70% NA
All Indica  2759 90.80% 4.50% 3.52% 1.16% NA
All Japonica  1512 99.70% 0.10% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 86.70% 5.40% 7.90% 0.00% NA
Indica II  465 91.20% 3.90% 4.09% 0.86% NA
Indica III  913 94.00% 3.50% 0.55% 1.97% NA
Indica Intermediate  786 90.10% 5.30% 3.31% 1.27% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.60% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 92.20% 4.40% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0802790437 T -> C LOC_Os08g05310.1 downstream_gene_variant ; 4677.0bp to feature; MODIFIER silent_mutation Average:50.441; most accessible tissue: Callus, score: 72.307 N N N N
vg0802790437 T -> C LOC_Os08g05320.2 intron_variant ; MODIFIER silent_mutation Average:50.441; most accessible tissue: Callus, score: 72.307 N N N N
vg0802790437 T -> C LOC_Os08g05320.3 intron_variant ; MODIFIER silent_mutation Average:50.441; most accessible tissue: Callus, score: 72.307 N N N N
vg0802790437 T -> DEL N N silent_mutation Average:50.441; most accessible tissue: Callus, score: 72.307 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0802790437 1.31E-06 NA mr1308 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