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Detailed information for vg0315011380:

Variant ID: vg0315011380 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15011380
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCTGCAGGCCTTCCTCCGGGAGGCCGACGCCAAGCGACGCGCCGTCTCCGACGAGGTCAACAAGGTGTGGCTGCTGCAGACGCGCGACGCCGTCTTCGA[C/T]
GCCGAGGACGCCCTCGATCATTTCTATCTCCGCGTCGATATGTCCAGGTATATATAGCTGCTACTAGATACTCCCTCTATTTTTTAATAGACGACGCCGT

Reverse complement sequence

ACGGCGTCGTCTATTAAAAAATAGAGGGAGTATCTAGTAGCAGCTATATATACCTGGACATATCGACGCGGAGATAGAAATGATCGAGGGCGTCCTCGGC[G/A]
TCGAAGACGGCGTCGCGCGTCTGCAGCAGCCACACCTTGTTGACCTCGTCGGAGACGGCGCGTCGCTTGGCGTCGGCCTCCCGGAGGAAGGCCTGCAGCC

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 98.20% 1.80% 0.00% 0.00% NA
All Indica  2759 97.10% 2.90% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 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 93.50% 6.50% 0.00% 0.00% NA
Indica III  913 94.90% 5.10% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 98.90% 1.10% 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
vg0315011380 C -> T LOC_Os03g26250.1 synonymous_variant ; p.Asp73Asp; LOW synonymous_codon Average:67.408; most accessible tissue: Minghui63 root, score: 82.818 N N N N