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Detailed information for vg0527589358:

Variant ID: vg0527589358 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27589358
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGTTGCTCCAAGCGGCGATGCAGCCGCCGTCCTCTTCCTCGCAGGCGTCGGCGTCGGCGTTGTTCCAGGGGGCGCCCGCACGTCGACCACCGCCTCCTC[G/T]
ATTTGGGGCCGACGGCCCTCTGCGCCCCGCACCGCCGCCTCGCCGTCGTCTCGGTCTGCCTCATCCTCAACCTCCCTACTCCGGTGTGCAGGCGACAAAG

Reverse complement sequence

CTTTGTCGCCTGCACACCGGAGTAGGGAGGTTGAGGATGAGGCAGACCGAGACGACGGCGAGGCGGCGGTGCGGGGCGCAGAGGGCCGTCGGCCCCAAAT[C/A]
GAGGAGGCGGTGGTCGACGTGCGGGCGCCCCCTGGAACAACGCCGACGCCGACGCCTGCGAGGAAGAGGACGGCGGCTGCATCGCCGCTTGGAGCAACGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(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
vg0527589358 G -> T LOC_Os05g48130.1 missense_variant ; p.Arg68Leu; MODERATE nonsynonymous_codon ; R68L Average:24.057; most accessible tissue: Minghui63 panicle, score: 53.77 unknown unknown DELETERIOUS 0.04