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Detailed information for vg0332252552:
| Variant ID: vg0332252552 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 32252552 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
GTGAAAGTGAAATCCCTTGGGAAGGGAACATGGGTGTAAGTTATAACAATCACCTGGGGGATTTGTGGACCGCTATGAAAGGGTGGTTGCTGTAGATGAG[G/A]
TTGCTGGAGAGGAGCAGGTGCTGGTTCCTGCAACTGTTTTGGAGTTCAAATTTGCAAGTTATAAGAAGAACAAAATTGACACTTCTCTTCAGCCATTCAT
Reverse complement sequence
ATGAATGGCTGAAGAGAAGTGTCAATTTTGTTCTTCTTATAACTTGCAAATTTGAACTCCAAAACAGTTGCAGGAACCAGCACCTGCTCCTCTCCAGCAA[C/T]
CTCATCTACAGCAACCACCCTTTCATAGCGGTCCACAAATCCCCCAGGTGATTGTTATAACTTACACCCATGTTCCCTTCCCAAGGGATTTCACTTTCAC
Allele Frequencies:
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0332252552 | G -> A | LOC_Os03g56630.1 | missense_variant ; p.Pro749Ser; MODERATE | nonsynonymous_codon ; P749S | Average:70.129; most accessible tissue: Callus, score: 88.391 | benign  |
0.173 |
TOLERATED | 0.07 |
| vg0332252552 | G -> A | LOC_Os03g56630.2 | missense_variant ; p.Pro747Ser; MODERATE | nonsynonymous_codon ; P747S | Average:70.129; most accessible tissue: Callus, score: 88.391 | benign |
0.173 |
TOLERATED | 0.07 |
| vg0332252552 | G -> DEL | LOC_Os03g56630.2 | N | frameshift_variant | Average:70.129; most accessible tissue: Callus, score: 88.391 | N | N | N | N |
| vg0332252552 | G -> DEL | LOC_Os03g56630.1 | N | frameshift_variant | Average:70.129; most accessible tissue: Callus, score: 88.391 | N | N | N | N |
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