Search for Variation information by Variation ID:
Detailed information for vg0409515347:
| Variant ID: vg0409515347 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515347 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTCCGAAAAATCCTTAGGCACTACTTTCTTGTTATAATGCCTAGCAA[C/T]
TCGTTCCTTATCTCTGGTAACCTTAGCAAGGGCTCGTAAACGCGATTGAACCAAGTCCTCCCTCTCATCGGCCATAAGGTTATAATATTCATCGGCTATC
Reverse complement sequence
GATAGCCGATGAATATTATAACCTTATGGCCGATGAGAGGGAGGACTTGGTTCAATCGCGTTTACGAGCCCTTGCTAAGGTTACCAGAGATAAGGAACGA[G/A]
TTGCTAGGCATTATAACAAGAAAGTAGTGCCTAAGGATTTTTCGGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTT
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 | 90.80% | 0.00% | 0.59% | 8.55% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 73.40% | 0.00% | 1.52% | 25.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 31.70% | 0.00% | 4.37% | 63.89% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 0.41% | 19.09% | NA |
| VI/Aromatic | 96 | 71.90% | 0.00% | 3.12% | 25.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 1.11% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515347 | C -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:23.576; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0409515347 | C -> T | LOC_Os04g17380.1 | missense_variant ; p.Val87Ile; MODERATE | nonsynonymous_codon ; V87I | Average:23.576; most accessible tissue: Minghui63 panicle, score: 34.226 | benign  |
0.547 |
TOLERATED | 0.37 |