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Detailed information for vg0321793118:

Variant ID: vg0321793118 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 21793118
Reference Allele: GGCAlternative Allele: G
Primary Allele: GGCSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCTCCCTCGCCGGAGCAGGTGGACTGGGCGGAAGGTGCAGTGATCTCCGCCCAGTCGGCGGCGGATAACATGGCGTCCTATGTGCTGGATCTCAGGAGG[GGC/G]
CTGGCCGTGTTCGCCGGGACAGGGAGGCCCGAGGAGGCGGTGCTCAGGAAGCACGTCGCGTGGGCCGACGCGCGCCGCGCGGAGGCGGTGGAGATCGCCT

Reverse complement sequence

AGGCGATCTCCACCGCCTCCGCGCGGCGCGCGTCGGCCCACGCGACGTGCTTCCTGAGCACCGCCTCCTCGGGCCTCCCTGTCCCGGCGAACACGGCCAG[GCC/C]
CCTCCTGAGATCCAGCACATAGGACGCCATGTTATCCGCCGCCGACTGGGCGGAGATCACTGCACCTTCCGCCCAGTCCACCTGCTCCGGCGAGGGAGGG

Allele Frequencies:

Populations Population SizeFrequency of GGC(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.20% 0.40% 0.36% 0.00% NA
All Indica  2759 98.80% 0.70% 0.51% 0.00% NA
All Japonica  1512 99.60% 0.20% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.60% 1.20% 1.18% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 98.80% 0.70% 0.55% 0.00% NA
Indica Intermediate  786 99.50% 0.30% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.41% 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
vg0321793118 GGC -> G LOC_Os03g39240.1 frameshift_variant ; p.Gly87fs; HIGH N Average:66.763; most accessible tissue: Zhenshan97 flower, score: 78.317 N N N N