Search for Variation information by Variation ID:
Detailed information for vg0802670352:
| Variant ID: vg0802670352 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 2670352 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AACCACAATAGTGCACGTGCTTTCCATCTCTTATAGTTTGAACCATCAAAGGCATGTGGTTTCAGTGTAGCAGCAAAGCCAACTACCGAAAATGACCTTT[C/T]
AGGTTTTTGGATTGTTGGAAATTTGGTCATAATTCGGCATATTTTAATCCAAAATAACAAGATAATAAACATGATATTTACAATAGGATTTGATCCAGTG
Reverse complement sequence
CACTGGATCAAATCCTATTGTAAATATCATGTTTATTATCTTGTTATTTTGGATTAAAATATGCCGAATTATGACCAAATTTCCAACAATCCAAAAACCT[G/A]
AAAGGTCATTTTCGGTAGTTGGCTTTGCTGCTACACTGAAACCACATGCCTTTGATGGTTCAAACTATAAGAGATGGAAAGCACGTGCACTATTGTGGTT
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 | 75.20% | 0.30% | 3.55% | 20.97% | NA |
| All Indica | 2759 | 67.90% | 0.40% | 4.71% | 27.00% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.07% | 0.26% | NA |
| Aus | 269 | 4.80% | 0.00% | 11.52% | 83.64% | NA |
| Indica I | 595 | 96.50% | 0.00% | 1.18% | 2.35% | NA |
| Indica II | 465 | 80.60% | 2.40% | 3.01% | 13.98% | NA |
| Indica III | 913 | 45.00% | 0.00% | 4.71% | 50.27% | NA |
| Indica Intermediate | 786 | 65.10% | 0.10% | 8.40% | 26.34% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 3.12% | 7.29% | NA |
| Intermediate | 90 | 85.60% | 0.00% | 3.33% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0802670352 | C -> T | LOC_Os08g05150.1 | missense_variant ; p.Glu110Lys; MODERATE | nonsynonymous_codon ; E110K | Average:10.62; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
1.176 |
TOLERATED | 0.21 |
| vg0802670352 | C -> DEL | LOC_Os08g05150.1 | N | frameshift_variant | Average:10.62; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |