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Detailed information for vg0321793066:

Variant ID: vg0321793066 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21793066
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATCACGGCCACAGCGCTGTCTGAAGCCACCGAGTACCTTGAGGACCCCGACCCTCCCTCGCCGGAGCAGGTGGACTGGGCGGAAGGTGCAGTGATCTC[C/T]
GCCCAGTCGGCGGCGGATAACATGGCGTCCTATGTGCTGGATCTCAGGAGGGGCCTGGCCGTGTTCGCCGGGACAGGGAGGCCCGAGGAGGCGGTGCTCA

Reverse complement sequence

TGAGCACCGCCTCCTCGGGCCTCCCTGTCCCGGCGAACACGGCCAGGCCCCTCCTGAGATCCAGCACATAGGACGCCATGTTATCCGCCGCCGACTGGGC[G/A]
GAGATCACTGCACCTTCCGCCCAGTCCACCTGCTCCGGCGAGGGAGGGTCGGGGTCCTCAAGGTACTCGGTGGCTTCAGACAGCGCTGTGGCCGTGATCT

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 99.60% 0.40% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 98.90% 1.10% 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  465 100.00% 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 96.60% 3.40% 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  90 100.00% 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
vg0321793066 C -> T LOC_Os03g39240.1 synonymous_variant ; p.Ser69Ser; LOW synonymous_codon Average:75.582; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N