Search for Variation information by Variation ID:
Detailed information for vg0142999406:
| Variant ID: vg0142999406 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42999406 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAGGGCCTGGCTCTTGATAGCGTGGCGTGGTTCAAAGTGCAAATCGAACTCAGAAAGTTCGATTGCCCATTTCACCACCCGTCCTGTACCCTCTTGATTA[T/C]
GCAAGATTTGACCGAGGGGGTAAGACGTAACTACTGTGACCCGATGCGCCTGGAAATAATGGCGCAGTTTCCTCGAGGCCATTAGAATAGCGTAAAGCAT
Reverse complement sequence
ATGCTTTACGCTATTCTAATGGCCTCGAGGAAACTGCGCCATTATTTCCAGGCGCATCGGGTCACAGTAGTTACGTCTTACCCCCTCGGTCAAATCTTGC[A/G]
TAATCAAGAGGGTACAGGACGGGTGGTGAAATGGGCAATCGAACTTTCTGAGTTCGATTTGCACTTTGAACCACGCCACGCTATCAAGAGCCAGGCCCTC
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 | 7.00% | 0.10% | 2.67% | 90.22% | NA |
| All Indica | 2759 | 0.50% | 0.20% | 3.04% | 96.27% | NA |
| All Japonica | 1512 | 20.10% | 0.00% | 0.33% | 79.56% | NA |
| Aus | 269 | 0.40% | 0.00% | 13.75% | 85.87% | NA |
| Indica I | 595 | 0.30% | 0.00% | 0.84% | 98.82% | NA |
| Indica II | 465 | 0.20% | 0.00% | 0.86% | 98.92% | NA |
| Indica III | 913 | 0.30% | 0.30% | 5.15% | 94.19% | NA |
| Indica Intermediate | 786 | 1.00% | 0.30% | 3.56% | 95.17% | NA |
| Temperate Japonica | 767 | 38.10% | 0.00% | 0.52% | 61.41% | NA |
| Tropical Japonica | 504 | 0.80% | 0.00% | 0.20% | 99.01% | NA |
| Japonica Intermediate | 241 | 3.30% | 0.00% | 0.00% | 96.68% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 13.30% | 0.00% | 0.00% | 86.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0142999406 | T -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:7.742; most accessible tissue: Callus, score: 13.366 | N | N | N | N |
| vg0142999406 | T -> C | LOC_Os01g74230.1 | missense_variant ; p.His1199Arg; MODERATE | nonsynonymous_codon ; H1199R | Average:7.742; most accessible tissue: Callus, score: 13.366 | benign  |
0.206 |
DELETERIOUS | 0.03 |