Search for Variation information by Variation ID:

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

Detailed information for vg0527589547:

Variant ID: vg0527589547 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27589547
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGGCGACAAAGTCCATGGAGGGACATGCTCCATGGGAGACACTGAATCCCCTCTTACACGAAGCTCCTGGCGTCGATTTCTCCATAGCTTATTCTGTGA[G/T]
TGATGAAGAATTCCTCCATAGGAGCAATTTCGGTAAAGCTATCCCTGATTCGTTCGATGTTTAGATTAATTTTCAGAGTGTTGCAGCCTGATCTGATGTC

Reverse complement sequence

GACATCAGATCAGGCTGCAACACTCTGAAAATTAATCTAAACATCGAACGAATCAGGGATAGCTTTACCGAAATTGCTCCTATGGAGGAATTCTTCATCA[C/A]
TCACAGAATAAGCTATGGAGAAATCGACGCCAGGAGCTTCGTGTAAGAGGGGATTCAGTGTCTCCCATGGAGCATGTCCCTCCATGGACTTTGTCGCCTG

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 97.20% 0.80% 2.03% 0.00% NA
All Indica  2759 97.40% 1.00% 1.67% 0.00% NA
All Japonica  1512 96.30% 0.70% 2.98% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.20% 0.50% 0.34% 0.00% NA
Indica II  465 90.10% 3.70% 6.24% 0.00% NA
Indica III  913 99.60% 0.00% 0.44% 0.00% NA
Indica Intermediate  786 97.70% 0.90% 1.40% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 90.90% 1.60% 7.54% 0.00% NA
Japonica Intermediate  241 96.70% 0.80% 2.49% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 96.70% 0.00% 3.33% 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
vg0527589547 G -> T LOC_Os05g48130.1 missense_variant ; p.Ser131Ile; MODERATE nonsynonymous_codon ; S131I Average:25.04; most accessible tissue: Zhenshan97 panicle, score: 39.652 possibly damaging 1.525 TOLERATED 0.05