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Detailed information for vg0527589353:

Variant ID: vg0527589353 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27589353
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCCGGCGTTGCTCCAAGCGGCGATGCAGCCGCCGTCCTCTTCCTCGCAGGCGTCGGCGTCGGCGTTGTTCCAGGGGGCGCCCGCACGTCGACCACCGCC[T/A]
CCTCGATTTGGGGCCGACGGCCCTCTGCGCCCCGCACCGCCGCCTCGCCGTCGTCTCGGTCTGCCTCATCCTCAACCTCCCTACTCCGGTGTGCAGGCGA

Reverse complement sequence

TCGCCTGCACACCGGAGTAGGGAGGTTGAGGATGAGGCAGACCGAGACGACGGCGAGGCGGCGGTGCGGGGCGCAGAGGGCCGTCGGCCCCAAATCGAGG[A/T]
GGCGGTGGTCGACGTGCGGGCGCCCCCTGGAACAACGCCGACGCCGACGCCTGCGAGGAAGAGGACGGCGGCTGCATCGCCGCTTGGAGCAACGCCGGCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.80% 3.20% 0.00% 0.00% NA
All Indica  2759 95.70% 4.30% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.30% 3.70% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 95.40% 4.60% 0.00% 0.00% NA
Indica Intermediate  786 92.90% 7.10% 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 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0527589353 T -> A LOC_Os05g48130.1 synonymous_variant ; p.Pro66Pro; LOW nonsynonymous_codon ; P66Q Average:24.596; most accessible tissue: Minghui63 panicle, score: 56.842 unknown unknown TOLERATED 0.09