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Detailed information for vg0327370669:

Variant ID: vg0327370669 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 27370669
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACACCGGCGAGCGCGCGGCGAGCACGGCGCGGTGTGCATGAAACGTCTCGCTGCCGACGGAGAACAACACGTCCGAGCCGTCGGCACGGTCCGCGATGTC[G/A]
TCGAGCTGGCCGTTGAGGTTCGACCGCGGGATGGGTATAGTGCCGTCGTCATCACCGGCATATAATATATATTTAAGAAAAGTAAAAATAGGGGGAAACA

Reverse complement sequence

TGTTTCCCCCTATTTTTACTTTTCTTAAATATATATTATATGCCGGTGATGACGACGGCACTATACCCATCCCGCGGTCGAACCTCAACGGCCAGCTCGA[C/T]
GACATCGCGGACCGTGCCGACGGCTCGGACGTGTTGTTCTCCGTCGGCAGCGAGACGTTTCATGCACACCGCGCCGTGCTCGCCGCGCGCTCGCCGGTGT

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 96.60% 2.80% 0.66% 0.00% NA
All Indica  2759 98.80% 1.00% 0.22% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 56.90% 34.90% 8.18% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 97.60% 2.40% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 0.60% 0.51% 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 92.70% 5.20% 2.08% 0.00% NA
Intermediate  90 94.40% 4.40% 1.11% 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
vg0327370669 G -> A LOC_Os03g48120.1 synonymous_variant ; p.Asp41Asp; LOW nonsynonymous_codon ; D41N Average:77.451; most accessible tissue: Zhenshan97 panicle, score: 87.764 benign 0.098 TOLERATED 0.06