Search for Variation information by Variation ID:
Detailed information for vg1007670790:
| Variant ID: vg1007670790 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670790 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 395. )
Flanking Sequence (100 bp) in Reference Genome:
TTCCTTGTCGGCTTTGACACCAGTGCGTAGATTCACCCAACGGCAGCGGAACAAAGGAACCTTGAACTTGACGTAGTTTAGCTCCCATATCTCCTCAATG[C/A]
GGCCGTAGTATGTGTTTGACCCAACTTGATCCTGGAATGCATCTATACGGACGTCGCTGTTTTGCACTGTGCTTTTGTCATCTTGTTTGACGGTGTAAAA
Reverse complement sequence
TTTTACACCGTCAAACAAGATGACAAAAGCACAGTGCAAAACAGCGACGTCCGTATAGATGCATTCCAGGATCAAGTTGGGTCAAACACATACTACGGCC[G/T]
CATTGAGGAGATATGGGAGCTAAACTACGTCAAGTTCAAGGTTCCTTTGTTCCGCTGCCGTTGGGTGAATCTACGCACTGGTGTCAAAGCCGACAAGGAA
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 | 80.60% | 0.10% | 5.37% | 13.97% | NA |
| All Indica | 2759 | 91.40% | 0.10% | 6.02% | 2.43% | NA |
| All Japonica | 1512 | 57.50% | 0.00% | 4.56% | 37.90% | NA |
| Aus | 269 | 96.30% | 0.00% | 3.35% | 0.37% | NA |
| Indica I | 595 | 97.10% | 0.00% | 2.18% | 0.67% | NA |
| Indica II | 465 | 83.90% | 0.00% | 10.97% | 5.16% | NA |
| Indica III | 913 | 94.20% | 0.30% | 4.71% | 0.77% | NA |
| Indica Intermediate | 786 | 88.40% | 0.00% | 7.51% | 4.07% | NA |
| Temperate Japonica | 767 | 68.40% | 0.00% | 3.13% | 28.42% | NA |
| Tropical Japonica | 504 | 31.50% | 0.00% | 7.14% | 61.31% | NA |
| Japonica Intermediate | 241 | 77.20% | 0.00% | 3.73% | 19.09% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 4.17% | 12.50% | NA |
| Intermediate | 90 | 85.60% | 0.00% | 6.67% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670790 | C -> A | LOC_Os10g14130.1 | missense_variant ; p.Arg374Leu; MODERATE | nonsynonymous_codon ; R374L | Average:11.755; most accessible tissue: Callus, score: 26.336 | benign  |
1.31 |
TOLERATED | 0.66 |
| vg1007670790 | C -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:11.755; most accessible tissue: Callus, score: 26.336 | N | N | N | N |