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Detailed information for vg0108457464:

Variant ID: vg0108457464 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 8457464
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGGGACACCTATAGGTATAAATACAAGCCCTCCTAGGAGGACAGGGGGAGAGACAACCACCATGAAAGTGAAAGACACCCATGACAATCAACACACGCC[T/C]
ACCAGAAGCCACAACATACAAGCCTACATACGCCAAGACACGCCGCCGGATATCGACTTGAAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATA

Reverse complement sequence

TATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTTCAAGTCGATATCCGGCGGCGTGTCTTGGCGTATGTAGGCTTGTATGTTGTGGCTTCTGGT[A/G]
GGCGTGTGTTGATTGTCATGGGTGTCTTTCACTTTCATGGTGGTTGTCTCTCCCCCTGTCCTCCTAGGAGGGCTTGTATTTATACCTATAGGTGTCCCCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.80% 7.00% 0.25% 0.00% NA
All Indica  2759 96.20% 3.70% 0.11% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 15.20% 81.80% 2.97% 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 95.10% 4.70% 0.22% 0.00% NA
Indica Intermediate  786 93.90% 6.00% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 1.11% 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
vg0108457464 T -> C LOC_Os01g15070.1 synonymous_variant ; p.Pro13Pro; LOW synonymous_codon Average:56.247; most accessible tissue: Minghui63 young leaf, score: 70.655 N N N N