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Detailed information for vg0324794178:

Variant ID: vg0324794178 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24794178
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTGTCAACATCAACATAAACCTGTGATAGAGGTTGCTGGGCTCGTCGATCGGACAAATTGCGTTGATTTGTCATGGTCATCTGAGAAGAGCCTTTCGAT[G/A]
GCATTGCTTTCCTAACCCCCAAAAAAAAGAAAGAAAAAAGAAATACACAATCCTTATCAGAGAGGGATTTACACCTACAGTGCCAATGAAACAAACTAGT

Reverse complement sequence

ACTAGTTTGTTTCATTGGCACTGTAGGTGTAAATCCCTCTCTGATAAGGATTGTGTATTTCTTTTTTCTTTCTTTTTTTTGGGGGTTAGGAAAGCAATGC[C/T]
ATCGAAAGGCTCTTCTCAGATGACCATGACAAATCAACGCAATTTGTCCGATCGACGAGCCCAGCAACCTCTATCACAGGTTTATGTTGATGTTGACAGT

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 65.00% 0.20% 8.89% 25.88% NA
All Indica  2759 48.10% 0.10% 8.92% 42.88% NA
All Japonica  1512 99.40% 0.00% 0.13% 0.46% NA
Aus  269 34.90% 1.90% 57.62% 5.58% NA
Indica I  595 78.20% 0.00% 5.04% 16.81% NA
Indica II  465 20.40% 0.00% 6.45% 73.12% NA
Indica III  913 35.50% 0.40% 15.12% 48.96% NA
Indica Intermediate  786 56.20% 0.00% 6.11% 37.66% NA
Temperate Japonica  767 99.50% 0.00% 0.13% 0.39% 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 92.70% 0.00% 5.21% 2.08% NA
Intermediate  90 68.90% 0.00% 13.33% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0324794178 G -> A LOC_Os03g44130.1 missense_variant ; p.Pro2Leu; MODERATE nonsynonymous_codon ; P2L Average:10.907; most accessible tissue: Zhenshan97 flower, score: 32.793 unknown unknown DELETERIOUS 0.02
vg0324794178 G -> DEL LOC_Os03g44130.1 N frameshift_variant Average:10.907; most accessible tissue: Zhenshan97 flower, score: 32.793 N N N N