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Detailed information for vg0114526638:

Variant ID: vg0114526638 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14526638
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTAGGGGAAATTTTAGAGTTGTGTTTTTCTGCTAGGGAATAGATGGTTCTCCAAGTTAGCTCTTATTTGTCGGACTGCAGGAATAGTTCTGCAAATAA[G/A]
AAACACATGATCAAAACTAGAAAAGAAGCACAAAATGAAACCAGACATCTAGGAACAAGCGGTTGAACCGTTGAAGATTCACCAAATCGAGAATATGGCA

Reverse complement sequence

TGCCATATTCTCGATTTGGTGAATCTTCAACGGTTCAACCGCTTGTTCCTAGATGTCTGGTTTCATTTTGTGCTTCTTTTCTAGTTTTGATCATGTGTTT[C/T]
TTATTTGCAGAACTATTCCTGCAGTCCGACAAATAAGAGCTAACTTGGAGAACCATCTATTCCCTAGCAGAAAAACACAACTCTAAAATTTCCCCTAAAC

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 94.70% 0.70% 0.83% 3.77% NA
All Indica  2759 93.50% 0.00% 0.18% 6.34% NA
All Japonica  1512 95.40% 2.30% 2.25% 0.07% NA
Aus  269 99.60% 0.00% 0.00% 0.37% NA
Indica I  595 95.60% 0.00% 0.00% 4.37% NA
Indica II  465 97.40% 0.00% 0.00% 2.58% NA
Indica III  913 92.00% 0.00% 0.33% 7.67% NA
Indica Intermediate  786 91.20% 0.00% 0.25% 8.52% NA
Temperate Japonica  767 91.00% 4.60% 4.30% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 0.00% 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
vg0114526638 G -> A LOC_Os01g25630.1 intron_variant ; MODIFIER silent_mutation Average:43.302; most accessible tissue: Zhenshan97 flower, score: 74.953 N N N N
vg0114526638 G -> DEL N N silent_mutation Average:43.302; most accessible tissue: Zhenshan97 flower, score: 74.953 N N N N