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Detailed information for vg0604192753:

Variant ID: vg0604192753 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4192753
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGCAACGGCGGCAAAGGCTCGCCGTGTCGATGAACATTGGTTGCTTGCTTGCTTACCTCCGACGACATGCTCGCCACCAGCGGCGCCATGCCGGCGGCG[C/G]
CGCCGAGCCGGCTCATGCTGAGAACCTGCGGTGTCAAAGGCAGTCACGATGGCATGTCTGATCGATCCTAGCTCACTGAGCTCAAACACACAGAATCGAT

Reverse complement sequence

ATCGATTCTGTGTGTTTGAGCTCAGTGAGCTAGGATCGATCAGACATGCCATCGTGACTGCCTTTGACACCGCAGGTTCTCAGCATGAGCCGGCTCGGCG[G/C]
CGCCGCCGGCATGGCGCCGCTGGTGGCGAGCATGTCGTCGGAGGTAAGCAAGCAAGCAACCAATGTTCATCGACACGGCGAGCCTTTGCCGCCGTTGCGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.20% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 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
vg0604192753 C -> G LOC_Os06g08500.1 missense_variant ; p.Gly220Ala; MODERATE nonsynonymous_codon ; G220A Average:67.583; most accessible tissue: Zhenshan97 young leaf, score: 78.347 possibly damaging 1.769 DELETERIOUS 0.00