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Detailed information for vg0321315554:

Variant ID: vg0321315554 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21315554
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACTAGCTAATGAATGGCCTTGAGATATACACTCACCGAGTAAGTCGACGAAGTTGTAGCCATTGCTGAACCTGCCGGTGGGCTTGCCCCCCGGGTAGTC[G/A]
ACGCCATTGTGAGGGTAGTTGGCCTTGAGCAGCGACGCCGGCAGGTAGTTGTTGTTCCCTACGTCCGCCTGCGAGTCGCCCAGCACGTACAGCGCCTCGA

Reverse complement sequence

TCGAGGCGCTGTACGTGCTGGGCGACTCGCAGGCGGACGTAGGGAACAACAACTACCTGCCGGCGTCGCTGCTCAAGGCCAACTACCCTCACAATGGCGT[C/T]
GACTACCCGGGGGGCAAGCCCACCGGCAGGTTCAGCAATGGCTACAACTTCGTCGACTTACTCGGTGAGTGTATATCTCAAGGCCATTCATTAGCTAGTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.60% 1.40% 0.00% 0.00% NA
All Indica  2759 99.20% 0.80% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 84.40% 15.60% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0321315554 G -> A LOC_Os03g38400.1 synonymous_variant ; p.Val70Val; LOW synonymous_codon Average:76.984; most accessible tissue: Minghui63 root, score: 82.511 N N N N