Search for Variation information by Variation ID:
Detailed information for vg0101920377:
| Variant ID: vg0101920377 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 1920377 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 372. )
Flanking Sequence (100 bp) in Reference Genome:
ACCACGGTATACAGACGGAAGACGTGACATAGTTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGA[C/T]
AGGCAGGCAGGACTGAGCCCCTAGCAGCAGGACACCGGCCCTGTGCCATGACATCTCGACTACCGGGCCGCAGCTCGTGTAGCCTTCATTTGCCCTGGAG
Reverse complement sequence
CTCCAGGGCAAATGAAGGCTACACGAGCTGCGGCCCGGTAGTCGAGATGTCATGGCACAGGGCCGGTGTCCTGCTGCTAGGGGCTCAGTCCTGCCTGCCT[G/A]
TCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAACTATGTCACGTCTTCCGTCTGTATACCGTGGT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.40% | 0.00% | 1.61% | 8.99% | NA |
| All Indica | 2759 | 92.20% | 0.00% | 2.36% | 5.40% | NA |
| All Japonica | 1512 | 81.60% | 0.10% | 0.53% | 17.79% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 83.50% | 0.00% | 3.19% | 13.28% | NA |
| Indica II | 465 | 91.20% | 0.00% | 3.44% | 5.38% | NA |
| Indica III | 913 | 97.50% | 0.00% | 1.31% | 1.20% | NA |
| Indica Intermediate | 786 | 93.40% | 0.00% | 2.29% | 4.33% | NA |
| Temperate Japonica | 767 | 89.00% | 0.00% | 0.13% | 10.82% | NA |
| Tropical Japonica | 504 | 78.20% | 0.20% | 0.79% | 20.83% | NA |
| Japonica Intermediate | 241 | 65.10% | 0.00% | 1.24% | 33.61% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 3.33% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0101920377 | C -> T | LOC_Os01g04310.1 | missense_variant ; p.Val19Ile; MODERATE | nonsynonymous_codon ; V19I | Average:6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | benign  |
0.621 |
DELETERIOUS | 0.02 |
| vg0101920377 | C -> DEL | LOC_Os01g04310.1 | N | frameshift_variant | Average:6.858; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |