Search for Variation information by Variation ID:
Detailed information for vg0512023233:
| Variant ID: vg0512023233 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12023233 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGAGTTATTCTGGGCAGGGACAACCTTCACGCGTCGGGGCTTCGGACACTTGTCAGCATAATGTCCTGGATCTCCACAGTTGAAACACACCACGGGCTTG[T/C]
TGCCTTGCTCCCTCTTGGCAGGTTGTTGCTGTGCTGGAGCTGCAACAGGACGTGGAGCTTGATTACGGATGTTGTTGCCAGCATTGTTGTTGAAGAACTG
Reverse complement sequence
CAGTTCTTCAACAACAATGCTGGCAACAACATCCGTAATCAAGCTCCACGTCCTGTTGCAGCTCCAGCACAGCAACAACCTGCCAAGAGGGAGCAAGGCA[A/G]
CAAGCCCGTGGTGTGTTTCAACTGTGGAGATCCAGGACATTATGCTGACAAGTGTCCGAAGCCCCGACGCGTGAAGGTTGTCCCTGCCCAGAATAACTCT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.20% | 4.80% | 6.07% | 1.95% | NA |
| All Indica | 2759 | 86.40% | 4.00% | 7.76% | 1.85% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 21.90% | 40.10% | 23.42% | 14.50% | NA |
| Indica I | 595 | 92.30% | 0.70% | 6.55% | 0.50% | NA |
| Indica II | 465 | 98.10% | 0.90% | 1.08% | 0.00% | NA |
| Indica III | 913 | 76.80% | 8.90% | 11.61% | 2.74% | NA |
| Indica Intermediate | 786 | 86.10% | 2.80% | 8.14% | 2.93% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 1.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 2.20% | 6.67% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512023233 | T -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:28.586; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 | N | N | N | N |
| vg0512023233 | T -> C | LOC_Os05g20480.1 | missense_variant ; p.Asn77Ser; MODERATE | nonsynonymous_codon | Average:28.586; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 | benign  |
-0.374 |
TOLERATED | 1.00 |