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Detailed information for vg0522746315:

Variant ID: vg0522746315 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 22746315
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTTCGGCGTGAGGGCGTCGTCGAGCAGGACGTTGGACGCCTTGAAGTCGCCGTACACCACCGGCGGGCTCGCCTTCTCGTGCAGGTACTCCAGCCCCTG[C/A]
GCTGCGCCGTACGCCACCTTCATCCTCGTGCACCAGTCCATCGGCTTCTTGTCCGCCGGCAAATCTGCCGACGACGACGATGCAACAATAACAGAACAAT

Reverse complement sequence

ATTGTTCTGTTATTGTTGCATCGTCGTCGTCGGCAGATTTGCCGGCGGACAAGAAGCCGATGGACTGGTGCACGAGGATGAAGGTGGCGTACGGCGCAGC[G/T]
CAGGGGCTGGAGTACCTGCACGAGAAGGCGAGCCCGCCGGTGGTGTACGGCGACTTCAAGGCGTCCAACGTCCTGCTCGACGACGCCCTCACGCCGAAGC

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 98.10% 1.60% 0.28% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 94.30% 4.80% 0.86% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 96.70% 3.00% 0.26% 0.00% NA
Tropical Japonica  504 93.80% 4.20% 1.98% 0.00% NA
Japonica Intermediate  241 87.60% 12.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0522746315 C -> A LOC_Os05g38770.1 synonymous_variant ; p.Ala190Ala; LOW synonymous_codon Average:67.731; most accessible tissue: Minghui63 young leaf, score: 82.907 N N N N