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Detailed information for vg0108239673:

Variant ID: vg0108239673 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 8239673
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTAATAGGCATCAGTATCTTCAACACAAGCTGCCTACGTTTGCCATGGCTGCCGACTGGTTTCTTCACTTCCATGGCTGCATGATTCTGCCAGTGTTGA[C/T]
TGGCCTTACCATCTTCATCGCCGGTCGTCTCGTCTGCTGCTGACTAGTGCCCTCACCTCTACGTCTGGTTTATACAGCTACCACTACTGATGGACATCAT

Reverse complement sequence

ATGATGTCCATCAGTAGTGGTAGCTGTATAAACCAGACGTAGAGGTGAGGGCACTAGTCAGCAGCAGACGAGACGACCGGCGATGAAGATGGTAAGGCCA[G/A]
TCAACACTGGCAGAATCATGCAGCCATGGAAGTGAAGAAACCAGTCGGCAGCCATGGCAAACGTAGGCAGCTTGTGTTGAAGATACTGATGCCTATTAGT

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 96.00% 0.20% 3.77% 0.00% NA
All Indica  2759 98.10% 0.30% 1.63% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 50.60% 0.40% 49.07% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 0.00% 1.08% 0.00% NA
Indica III  913 96.90% 0.80% 2.30% 0.00% NA
Indica Intermediate  786 97.50% 0.10% 2.42% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 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  90 100.00% 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
vg0108239673 C -> T LOC_Os01g14730.1 missense_variant ; p.Thr253Ile; MODERATE nonsynonymous_codon ; T253I Average:43.495; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 benign -0.986 TOLERATED 1.00