Search for Variation information by Variation ID:
Detailed information for vg0410565300:
| Variant ID: vg0410565300 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10565300 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTATTCTCGTGTGTGAGCATACTCCCGGTCACTCAGCATGTAGTAGGCTTGTCTTTCCCGATCGTCGACAAGGTCGAGGTCGGCGTCATTCAAGAGACGT[C/G]
GTGGAGCTTCGGCATCCTCCATCGAGACTATTGGCGGCTATTAAATGCCGATTCTATACTACCAACATATGCGTAAAGTTCAGATAATAAAACATCCAAC
Reverse complement sequence
GTTGGATGTTTTATTATCTGAACTTTACGCATATGTTGGTAGTATAGAATCGGCATTTAATAGCCGCCAATAGTCTCGATGGAGGATGCCGAAGCTCCAC[G/C]
ACGTCTCTTGAATGACGCCGACCTCGACCTTGTCGACGATCGGGAAAGACAAGCCTACTACATGCTGAGTGACCGGGAGTATGCTCACACACGAGAATAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.70% | 0.20% | 0.66% | 59.44% | NA |
| All Indica | 2759 | 8.60% | 0.40% | 1.01% | 90.00% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.00% | 0.86% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.37% | 98.88% | NA |
| Indica I | 595 | 5.50% | 0.00% | 1.18% | 93.28% | NA |
| Indica II | 465 | 25.40% | 0.20% | 0.65% | 73.76% | NA |
| Indica III | 913 | 2.40% | 0.70% | 1.20% | 95.73% | NA |
| Indica Intermediate | 786 | 8.30% | 0.40% | 0.89% | 90.46% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 58.90% | 0.00% | 2.22% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565300 | C -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:9.854; most accessible tissue: Callus, score: 40.877 | N | N | N | N |
| vg0410565300 | C -> G | LOC_Os04g19010.1 | missense_variant ; p.Arg8Pro; MODERATE | nonsynonymous_codon ; R8P | Average:9.854; most accessible tissue: Callus, score: 40.877 | probably damaging  |
2.235 |
TOLERATED | 0.21 |