Search for Variation information by Variation ID:
Detailed information for vg0807399608:
| Variant ID: vg0807399608 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7399608 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCGAGGGGACCGTCTGGGTCGATCACGACATTCCAGGGATATGAGATCAATGGGTACACATTCTACACGAGAGCCCAAGACATGAAGAGCACGAACCAA[A/G]
ACAGCGCTGTTCGTGTCGATGCCATGGGACACGATGGAACAACTGCCACGTATTACGGTGCCATCGAGGACATATGGGAACTTGACTATGGTCCTCTCAA
Reverse complement sequence
TTGAGAGGACCATAGTCAAGTTCCCATATGTCCTCGATGGCACCGTAATACGTGGCAGTTGTTCCATCGTGTCCCATGGCATCGACACGAACAGCGCTGT[T/C]
TTGGTTCGTGCTCTTCATGTCTTGGGCTCTCGTGTAGAATGTGTACCCATTGATCTCATATCCCTGGAATGTCGTGATCGACCCAGACGGTCCCCTCGCC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.00% | 0.50% | 2.98% | 63.50% | NA |
| All Indica | 2759 | 14.50% | 0.00% | 3.04% | 82.49% | NA |
| All Japonica | 1512 | 73.30% | 1.50% | 3.37% | 21.83% | NA |
| Aus | 269 | 3.00% | 0.00% | 1.49% | 95.54% | NA |
| Indica I | 595 | 33.30% | 0.00% | 3.53% | 63.19% | NA |
| Indica II | 465 | 15.30% | 0.00% | 3.44% | 81.29% | NA |
| Indica III | 913 | 2.50% | 0.00% | 1.53% | 95.95% | NA |
| Indica Intermediate | 786 | 13.60% | 0.00% | 4.20% | 82.19% | NA |
| Temperate Japonica | 767 | 55.10% | 3.00% | 4.17% | 37.68% | NA |
| Tropical Japonica | 504 | 94.40% | 0.00% | 2.78% | 2.78% | NA |
| Japonica Intermediate | 241 | 86.70% | 0.00% | 2.07% | 11.20% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 2.08% | 93.75% | NA |
| Intermediate | 90 | 45.60% | 1.10% | 0.00% | 53.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807399608 | A -> G | LOC_Os08g12500.1 | missense_variant ; p.Asn884Asp; MODERATE | nonsynonymous_codon | Average:5.605; most accessible tissue: Minghui63 flower, score: 10.335 | possibly damaging  |
1.732 |
DELETERIOUS | 0.00 |
| vg0807399608 | A -> DEL | LOC_Os08g12500.1 | N | frameshift_variant | Average:5.605; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |