Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0527589454:

Variant ID: vg0527589454 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27589454
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCGATTTGGGGCCGACGGCCCTCTGCGCCCCGCACCGCCGCCTCGCCGTCGTCTCGGTCTGCCTCATCCTCAACCTCCCTACTCCGGTGTGCAGGCGA[C/T]
AAAGTCCATGGAGGGACATGCTCCATGGGAGACACTGAATCCCCTCTTACACGAAGCTCCTGGCGTCGATTTCTCCATAGCTTATTCTGTGAGTGATGAA

Reverse complement sequence

TTCATCACTCACAGAATAAGCTATGGAGAAATCGACGCCAGGAGCTTCGTGTAAGAGGGGATTCAGTGTCTCCCATGGAGCATGTCCCTCCATGGACTTT[G/A]
TCGCCTGCACACCGGAGTAGGGAGGTTGAGGATGAGGCAGACCGAGACGACGGCGAGGCGGCGGTGCGGGGCGCAGAGGGCCGTCGGCCCCAAATCGAGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.30% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 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  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 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 84.40% 14.60% 1.04% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0527589454 C -> T LOC_Os05g48130.1 missense_variant ; p.Thr100Ile; MODERATE nonsynonymous_codon ; T100I Average:24.17; most accessible tissue: Minghui63 panicle, score: 42.799 benign 1.489 TOLERATED 0.06