Search for Variation information by Variation ID:
Detailed information for vg0807399716:
| Variant ID: vg0807399716 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7399716 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGTTCGTGTCGATGCCATGGGACACGATGGAACAACTGCCACGTATTACGGTGCCATCGAGGACATATGGGAACTTGACTATGGTCCTCTCAAGGTTCCT[C/A]
TGTTCCGGTGCCAATGGGTTAGGTTGACTGATGGAGGCGTAATGATTGATGACAGTGGGATGACAACTGTTGACCTTAACAAGGTTGGATACTCGGATGA
Reverse complement sequence
TCATCCGAGTATCCAACCTTGTTAAGGTCAACAGTTGTCATCCCACTGTCATCAATCATTACGCCTCCATCAGTCAACCTAACCCATTGGCACCGGAACA[G/T]
AGGAACCTTGAGAGGACCATAGTCAAGTTCCCATATGTCCTCGATGGCACCGTAATACGTGGCAGTTGTTCCATCGTGTCCCATGGCATCGACACGAACA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.10% | 0.10% | 3.41% | 61.38% | NA |
| All Indica | 2759 | 14.90% | 0.20% | 3.41% | 81.44% | NA |
| All Japonica | 1512 | 78.80% | 0.00% | 3.31% | 17.92% | NA |
| Aus | 269 | 3.70% | 0.00% | 4.09% | 92.19% | NA |
| Indica I | 595 | 35.00% | 0.30% | 2.52% | 62.18% | NA |
| Indica II | 465 | 16.30% | 0.00% | 4.30% | 79.35% | NA |
| Indica III | 913 | 1.60% | 0.20% | 2.63% | 95.51% | NA |
| Indica Intermediate | 786 | 14.40% | 0.30% | 4.45% | 80.92% | NA |
| Temperate Japonica | 767 | 62.80% | 0.00% | 5.08% | 32.07% | NA |
| Tropical Japonica | 504 | 96.20% | 0.00% | 1.98% | 1.79% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 0.41% | 6.64% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 4.17% | 90.62% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0807399716 | C -> A | LOC_Os08g12500.1 | missense_variant ; p.Leu920Met; MODERATE | nonsynonymous_codon ; L920M | Average:5.692; most accessible tissue: Minghui63 flower, score: 10.335 | probably damaging  |
2.661 |
DELETERIOUS | 0.00 |
| vg0807399716 | C -> DEL | LOC_Os08g12500.1 | N | frameshift_variant | Average:5.692; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |