Search for Variation information by Variation ID:
Detailed information for vg0128724247:
| Variant ID: vg0128724247 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724247 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GATGCAACGTGGGAGCACGGTTTGTCTGCTGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGT[C/T]
GCACGTCTGTCCTTCTTCATACAATGACTTCTTTGCAATGGTTGCGATGAAGCCTGGAATGTATCTAGCCGGGACTGGCGTGCTAACTCCAGGAGTTAGC
Reverse complement sequence
GCTAACTCCTGGAGTTAGCACGCCAGTCCCGGCTAGATACATTCCAGGCTTCATCGCAACCATTGCAAAGAAGTCATTGTATGAAGAAGGACAGACGTGC[G/A]
ACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCAGCAGACAAACCGTGCTCCCACGTTGCATC
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 | 70.00% | 0.10% | 3.15% | 26.77% | NA |
| All Indica | 2759 | 60.50% | 0.10% | 1.49% | 37.88% | NA |
| All Japonica | 1512 | 88.80% | 0.00% | 0.93% | 10.25% | NA |
| Aus | 269 | 66.90% | 0.00% | 30.48% | 2.60% | NA |
| Indica I | 595 | 50.60% | 0.00% | 1.34% | 48.07% | NA |
| Indica II | 465 | 52.30% | 0.00% | 1.08% | 46.67% | NA |
| Indica III | 913 | 72.50% | 0.20% | 0.66% | 26.62% | NA |
| Indica Intermediate | 786 | 59.00% | 0.10% | 2.80% | 38.04% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 69.80% | 0.00% | 2.58% | 27.58% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724247 | C -> T | LOC_Os01g49990.1 | missense_variant ; p.Ser47Leu; MODERATE | nonsynonymous_codon ; S47L | Average:11.799; most accessible tissue: Callus, score: 22.262 | benign  |
-1.115 |
TOLERATED | 1.00 |
| vg0128724247 | C -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:11.799; most accessible tissue: Callus, score: 22.262 | N | N | N | N |