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Detailed information for vg0216160840:

Variant ID: vg0216160840 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16160840
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTAGCTGTCTTCGATGTGCGCTTCACGACGGTTTTATTCTCGCACGATGGGCACAGGATCAATGGTACCTTCTTCCGGCGAGTACAAGCGGAGGCCGG[G/T]
CTTGAAGAAGCCATGGGGGCCGCGACCAGTCCTTGGCTACCACCCGTCATGGCCTCCCCGCCGCACTTGGTTGCCTCCTGCCGTCGCCTCGCCACCGCAG

Reverse complement sequence

CTGCGGTGGCGAGGCGACGGCAGGAGGCAACCAAGTGCGGCGGGGAGGCCATGACGGGTGGTAGCCAAGGACTGGTCGCGGCCCCCATGGCTTCTTCAAG[C/A]
CCGGCCTCCGCTTGTACTCGCCGGAAGAAGGTACCATTGATCCTGTGCCCATCGTGCGAGAATAAAACCGTCGTGAAGCGCACATCGAAGACAGCTAGTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.80% 6.10% 0.17% 0.00% NA
All Indica  2759 89.50% 10.30% 0.25% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.00% 0.67% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 77.30% 22.60% 0.11% 0.00% NA
Indica Intermediate  786 91.50% 8.30% 0.25% 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 96.70% 2.20% 1.11% 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
vg0216160840 G -> T LOC_Os02g27430.1 missense_variant ; p.Ser17Arg; MODERATE nonsynonymous_codon ; S17R Average:60.186; most accessible tissue: Zhenshan97 young leaf, score: 86.383 unknown unknown DELETERIOUS 0.01