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Detailed information for vg0512023367:

Variant ID: vg0512023367 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 12023367
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTGGAGCTGCAACAGGACGTGGAGCTTGATTACGGATGTTGTTGCCAGCATTGTTGTTGAAGAACTGACGCTGCGGACGAACAACAGACGAAGAACCTCC[C/A]
TGTGGCATGGGCTGGGGTCCTAAAGTAAGACGCGGCTTCTGATTATTTCCCTGTTGTGTCTTGAATTGAGCAATCCGACGTTTCTTCTGCTCCATGCGAT

Reverse complement sequence

ATCGCATGGAGCAGAAGAAACGTCGGATTGCTCAATTCAAGACACAACAGGGAAATAATCAGAAGCCGCGTCTTACTTTAGGACCCCAGCCCATGCCACA[G/T]
GGAGGTTCTTCGTCTGTTGTTCGTCCGCAGCGTCAGTTCTTCAACAACAATGCTGGCAACAACATCCGTAATCAAGCTCCACGTCCTGTTGCAGCTCCAG

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 87.30% 0.40% 5.37% 6.94% NA
All Indica  2759 86.50% 0.40% 6.96% 6.16% NA
All Japonica  1512 99.70% 0.00% 0.07% 0.26% NA
Aus  269 23.00% 2.20% 20.07% 54.65% NA
Indica I  595 92.10% 0.00% 2.02% 5.88% NA
Indica II  465 98.30% 0.00% 0.65% 1.08% NA
Indica III  913 77.20% 0.70% 15.22% 6.90% NA
Indica Intermediate  786 86.00% 0.60% 4.83% 8.52% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.00% 0.20% 0.60% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 95.80% 0.00% 3.12% 1.04% NA
Intermediate  90 88.90% 0.00% 4.44% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0512023367 C -> DEL LOC_Os05g20480.1 N frameshift_variant Average:26.557; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 N N N N
vg0512023367 C -> A LOC_Os05g20480.1 missense_variant ; p.Gln32His; MODERATE nonsynonymous_codon ; Q32H Average:26.557; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 benign 0.026 TOLERATED 0.10