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Detailed information for vg0321793042:

Variant ID: vg0321793042 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21793042
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGCCGACGACCGAGAGTGTGAGGAGATCACGGCCACAGCGCTGTCTGAAGCCACCGAGTACCTTGAGGACCCCGACCCTCCCTCGCCGGAGCAGGTGGA[C/A]
TGGGCGGAAGGTGCAGTGATCTCCGCCCAGTCGGCGGCGGATAACATGGCGTCCTATGTGCTGGATCTCAGGAGGGGCCTGGCCGTGTTCGCCGGGACAG

Reverse complement sequence

CTGTCCCGGCGAACACGGCCAGGCCCCTCCTGAGATCCAGCACATAGGACGCCATGTTATCCGCCGCCGACTGGGCGGAGATCACTGCACCTTCCGCCCA[G/T]
TCCACCTGCTCCGGCGAGGGAGGGTCGGGGTCCTCAAGGTACTCGGTGGCTTCAGACAGCGCTGTGGCCGTGATCTCCTCACACTCTCGGTCGTCGGCCT

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 97.70% 2.30% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 93.10% 6.90% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 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 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 95.00% 5.00% 0.00% 0.00% NA
Japonica Intermediate  241 68.50% 31.50% 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
vg0321793042 C -> A LOC_Os03g39240.1 missense_variant ; p.Asp61Glu; MODERATE nonsynonymous_codon ; D61G Average:76.507; most accessible tissue: Minghui63 panicle, score: 84.005 possibly damaging -1.911 TOLERATED 0.77