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Detailed information for vg0108457673:

Variant ID: vg0108457673 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 8457673
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATACGAAAGCGCTATCTCTGATCTCGCCGGGCACAGATTCGAGGAGGAAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGACATGTCCA[C/T]
AACAGTTAGATAGGCTACCCACATATTGTACTGGTGTGATTATGGTGAATAAAAGCAATACCGGCTTCGGCCAACAGGATGTAGGGTTATTACCTGACAA

Reverse complement sequence

TTGTCAGGTAATAACCCTACATCCTGTTGGCCGAAGCCGGTATTGCTTTTATTCACCATAATCACACCAGTACAATATGTGGGTAGCCTATCTAACTGTT[G/A]
TGGACATGTCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTTCCTCCTCGAATCTGTGCCCGGCGAGATCAGAGATAGCGCTTTCGTATCT

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 92.90% 7.10% 0.02% 0.00% NA
All Indica  2759 96.30% 3.70% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 15.20% 84.40% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 95.30% 4.70% 0.00% 0.00% NA
Indica Intermediate  786 94.00% 6.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0108457673 C -> T LOC_Os01g15070.1 missense_variant ; p.Thr83Ile; MODERATE nonsynonymous_codon ; T83I Average:57.517; most accessible tissue: Zhenshan97 panicle, score: 75.67 possibly damaging 1.851 TOLERATED 0.08