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Detailed information for vg1218481396:

Variant ID: vg1218481396 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18481396
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAACCCCGCCGGAAGTCGCCGTCACCGTG[A/C]
AGGCCGAACCGTTGCCATGTTTTGATCTCCAACGAAGCTTTGCCGTCGACTCCGTGGTCGCCGGACCTCGCCGTATCCACTGTCGGCATCGCAGCAGTGA

Reverse complement sequence

TCACTGCTGCGATGCCGACAGTGGATACGGCGAGGTCCGGCGACCACGGAGTCGACGGCAAAGCTTCGTTGGAGATCAAAACATGGCAACGGTTCGGCCT[T/G]
CACGGTGACGGCGACTTCCGGCGGGGTTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 13.10% 0.30% 2.92% 83.66% NA
All Indica  2759 2.10% 0.50% 3.26% 94.06% NA
All Japonica  1512 35.10% 0.00% 0.46% 64.48% NA
Aus  269 1.50% 0.00% 13.75% 84.76% NA
Indica I  595 3.20% 0.00% 2.18% 94.62% NA
Indica II  465 3.00% 0.00% 3.01% 93.98% NA
Indica III  913 0.30% 1.60% 3.07% 94.96% NA
Indica Intermediate  786 2.90% 0.00% 4.45% 92.62% NA
Temperate Japonica  767 59.60% 0.00% 0.26% 40.16% NA
Tropical Japonica  504 3.00% 0.00% 0.40% 96.63% NA
Japonica Intermediate  241 24.10% 0.00% 1.24% 74.69% NA
VI/Aromatic  96 0.00% 0.00% 1.04% 98.96% NA
Intermediate  90 27.80% 1.10% 3.33% 67.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218481396 A -> C LOC_Os12g30780.1 synonymous_variant ; p.Leu47Leu; LOW nonsynonymous_codon ; L47P Average:23.895; most accessible tissue: Minghui63 young leaf, score: 42.042 unknown unknown DELETERIOUS 0.02
vg1218481396 A -> DEL LOC_Os12g30780.1 N frameshift_variant Average:23.895; most accessible tissue: Minghui63 young leaf, score: 42.042 N N N N