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Detailed information for vg0527589451:

Variant ID: vg0527589451 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27589451
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCCTCGATTTGGGGCCGACGGCCCTCTGCGCCCCGCACCGCCGCCTCGCCGTCGTCTCGGTCTGCCTCATCCTCAACCTCCCTACTCCGGTGTGCAGG[C/A]
GACAAAGTCCATGGAGGGACATGCTCCATGGGAGACACTGAATCCCCTCTTACACGAAGCTCCTGGCGTCGATTTCTCCATAGCTTATTCTGTGAGTGAT

Reverse complement sequence

ATCACTCACAGAATAAGCTATGGAGAAATCGACGCCAGGAGCTTCGTGTAAGAGGGGATTCAGTGTCTCCCATGGAGCATGTCCCTCCATGGACTTTGTC[G/T]
CCTGCACACCGGAGTAGGGAGGTTGAGGATGAGGCAGACCGAGACGACGGCGAGGCGGCGGTGCGGGGCGCAGAGGGCCGTCGGCCCCAAATCGAGGAGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 1.50% 0.85% 0.00% NA
All Indica  2759 96.00% 2.60% 1.30% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 0.00% 1.18% 0.00% NA
Indica II  465 98.90% 0.40% 0.65% 0.00% NA
Indica III  913 92.70% 6.40% 0.99% 0.00% NA
Indica Intermediate  786 96.20% 1.70% 2.16% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 2.22% 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
vg0527589451 C -> A LOC_Os05g48130.1 missense_variant ; p.Ala99Glu; MODERATE nonsynonymous_codon ; A99E Average:24.17; most accessible tissue: Minghui63 panicle, score: 42.799 benign 1.487 DELETERIOUS 0.00