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Detailed information for vg1123253132:

Variant ID: vg1123253132 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23253132
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTGTGCAGGGCGGCCATCTTGTCGATCTCCCGGCGCTGCTCCGGCGAGAGGTGCTTCAGGTCGTCGTCGGAGAAGACCGGCCATTGCACCCTCTCGAAC[G/C]
CCAGGATGGAGTCGACGTACCCCTGCGCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGCCGGCGGCGGTGGCGGCCGCCGCCGCCGTCGTCTT

Reverse complement sequence

AAGACGACGGCGGCGGCGGCCGCCACCGCCGCCGGCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGCGCAGGGGTACGTCGACTCCATCCTGG[C/G]
GTTCGAGAGGGTGCAATGGCCGGTCTTCTCCGACGACGACCTGAAGCACCTCTCGCCGGAGCAGCGCCGGGAGATCGACAAGATGGCCGCCCTGCACAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.70% 2.30% 0.00% 0.00% NA
All Indica  2759 97.00% 3.00% 0.00% 0.00% NA
All Japonica  1512 98.60% 1.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 95.20% 4.80% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 95.80% 4.20% 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 97.80% 2.20% 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
vg1123253132 G -> C LOC_Os11g39060.1 missense_variant ; p.Ala47Gly; MODERATE nonsynonymous_codon ; A47G Average:67.246; most accessible tissue: Minghui63 root, score: 82.967 unknown unknown DELETERIOUS 0.03