Search for Variation information by Variation ID:
Detailed information for vg0128724229:
| Variant ID: vg0128724229 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724229 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCCACTTCGCTGGAAGCAGATGCAACGTGGGAGCACGGTTTGTCTGCTGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCA[C/T]
GTGTCAGTTTAGCATGTCGCACGTCTGTCCTTCTTCATACAATGACTTCTTTGCAATGGTTGCGATGAAGCCTGGAATGTATCTAGCCGGGACTGGCGTG
Reverse complement sequence
CACGCCAGTCCCGGCTAGATACATTCCAGGCTTCATCGCAACCATTGCAAAGAAGTCATTGTATGAAGAAGGACAGACGTGCGACATGCTAAACTGACAC[G/A]
TGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCAGCAGACAAACCGTGCTCCCACGTTGCATCTGCTTCCAGCGAAGTGGA
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 | 69.10% | 0.60% | 3.47% | 26.89% | NA |
| All Indica | 2759 | 58.90% | 1.00% | 2.17% | 37.95% | NA |
| All Japonica | 1512 | 88.80% | 0.00% | 0.73% | 10.52% | NA |
| Aus | 269 | 67.30% | 0.00% | 30.11% | 2.60% | NA |
| Indica I | 595 | 50.40% | 0.20% | 1.34% | 48.07% | NA |
| Indica II | 465 | 52.30% | 0.00% | 1.08% | 46.67% | NA |
| Indica III | 913 | 69.30% | 2.00% | 1.86% | 26.83% | NA |
| Indica Intermediate | 786 | 57.10% | 1.00% | 3.82% | 38.04% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 69.60% | 0.00% | 1.98% | 28.37% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 0.41% | 4.56% | NA |
| VI/Aromatic | 96 | 50.00% | 0.00% | 9.38% | 40.62% | NA |
| Intermediate | 90 | 75.60% | 0.00% | 3.33% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724229 | C -> T | LOC_Os01g49990.1 | missense_variant ; p.Thr41Met; MODERATE | nonsynonymous_codon ; T41M | Average:11.72; most accessible tissue: Callus, score: 22.262 | benign  |
0.748 |
TOLERATED | 0.05 |
| vg0128724229 | C -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:11.72; most accessible tissue: Callus, score: 22.262 | N | N | N | N |