Search for Variation information by Variation ID:
Detailed information for vg0128724214:
| Variant ID: vg0128724214 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724214 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGGGTCATACCTACCTCCACTTCGCTGGAAGCAGATGCAACGTGGGAGCACGGTTTGTCTGCTGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGT[C/T]
ATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCACGTCTGTCCTTCTTCATACAATGACTTCTTTGCAATGGTTGCGATGAAGCCTGGAATGTATCTA
Reverse complement sequence
TAGATACATTCCAGGCTTCATCGCAACCATTGCAAAGAAGTCATTGTATGAAGAAGGACAGACGTGCGACATGCTAAACTGACACGTGGTGGACAAGAAT[G/A]
ACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCAGCAGACAAACCGTGCTCCCACGTTGCATCTGCTTCCAGCGAAGTGGAGGTAGGTATGACCCA
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 | 69.60% | 0.30% | 3.66% | 26.51% | NA |
| All Indica | 2759 | 60.80% | 0.00% | 2.14% | 37.08% | NA |
| All Japonica | 1512 | 87.20% | 0.70% | 1.26% | 10.85% | NA |
| Aus | 269 | 66.50% | 0.00% | 30.86% | 2.60% | NA |
| Indica I | 595 | 50.90% | 0.00% | 1.01% | 48.07% | NA |
| Indica II | 465 | 52.30% | 0.00% | 1.72% | 46.02% | NA |
| Indica III | 913 | 72.70% | 0.00% | 2.19% | 25.08% | NA |
| Indica Intermediate | 786 | 59.40% | 0.00% | 3.18% | 37.40% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 65.30% | 2.00% | 3.37% | 29.37% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.83% | 4.56% | NA |
| VI/Aromatic | 96 | 50.00% | 0.00% | 8.33% | 41.67% | NA |
| Intermediate | 90 | 71.10% | 3.30% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724214 | C -> T | LOC_Os01g49990.1 | missense_variant ; p.Ser36Leu; MODERATE | nonsynonymous_codon ; S36L | Average:10.968; most accessible tissue: Callus, score: 22.262 | possibly damaging  |
1.746 |
DELETERIOUS | 0.00 |
| vg0128724214 | C -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:10.968; most accessible tissue: Callus, score: 22.262 | N | N | N | N |