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Detailed information for vg0825762523:

Variant ID: vg0825762523 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25762523
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATATATACGAACTTACCTGCAACTAATTTCTCCACCCCCCAACACAACAGCACTCCACACACAATTACACAACAATGGCGTCCGAACAACAACGCCGGC[G/C]
ATCACCACCTACCATCCTCGCCGCCATCCTTCTTCTCTCCTTCTTGGCGACGGCCAACCTCGCCGGCGCCATCGATCCAGCCGGAAGGAGACGGAACGTG

Reverse complement sequence

CACGTTCCGTCTCCTTCCGGCTGGATCGATGGCGCCGGCGAGGTTGGCCGTCGCCAAGAAGGAGAGAAGAAGGATGGCGGCGAGGATGGTAGGTGGTGAT[C/G]
GCCGGCGTTGTTGTTCGGACGCCATTGTTGTGTAATTGTGTGTGGAGTGCTGTTGTGTTGGGGGGTGGAGAAATTAGTTGCAGGTAAGTTCGTATATATA

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 98.80% 1.20% 0.00% 0.00% NA
All Indica  2759 98.10% 1.90% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 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 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 96.10% 3.90% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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
vg0825762523 G -> C LOC_Os08g40690.1 missense_variant ; p.Arg9Pro; MODERATE nonsynonymous_codon ; R9P Average:76.006; most accessible tissue: Callus, score: 94.222 unknown unknown DELETERIOUS 0.05