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Detailed information for vg0318608296:

Variant ID: vg0318608296 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18608296
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCAGCCTCTGCCCACACAGAAACGCAAGGGAGAGAAAAACAACACACACACACACACACACACTGTTAAATAAACCGACAGCAAATTGGGGGGGCAACAC[G/A]
AAATCGGGCGCGCCACCCACCCACCCACCTTCCTCCTCGTCGCTGCGCCCCTGGACGATCTGCGCCTTCACCTCCTCGAACAGCAGCGGCTCGAACACAG

Reverse complement sequence

CTGTGTTCGAGCCGCTGCTGTTCGAGGAGGTGAAGGCGCAGATCGTCCAGGGGCGCAGCGACGAGGAGGAAGGTGGGTGGGTGGGTGGCGCGCCCGATTT[C/T]
GTGTTGCCCCCCCAATTTGCTGTCGGTTTATTTAACAGTGTGTGTGTGTGTGTGTGTGTTGTTTTTCTCTCCCTTGCGTTTCTGTGTGGGCAGAGGCTGG

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 84.70% 3.70% 10.98% 0.61% NA
All Indica  2759 75.10% 6.30% 18.16% 0.36% NA
All Japonica  1512 97.90% 0.00% 0.93% 1.19% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 72.80% 3.20% 24.03% 0.00% NA
Indica II  465 47.50% 13.10% 37.85% 1.51% NA
Indica III  913 91.50% 4.80% 3.72% 0.00% NA
Indica Intermediate  786 74.30% 6.50% 18.83% 0.38% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 94.20% 0.00% 2.18% 3.57% NA
Japonica Intermediate  241 98.80% 0.00% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 1.10% 4.44% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0318608296 G -> A LOC_Os03g32540.1 upstream_gene_variant ; 2897.0bp to feature; MODIFIER silent_mutation Average:22.237; most accessible tissue: Zhenshan97 panicle, score: 43.098 N N N N
vg0318608296 G -> A LOC_Os03g32526.1 intron_variant ; MODIFIER silent_mutation Average:22.237; most accessible tissue: Zhenshan97 panicle, score: 43.098 N N N N
vg0318608296 G -> DEL N N silent_mutation Average:22.237; most accessible tissue: Zhenshan97 panicle, score: 43.098 N N N N