Search for Variation information by Variation ID:
Detailed information for vg1007670943:
| Variant ID: vg1007670943 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670943 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 409. )
Flanking Sequence (100 bp) in Reference Genome:
GTCGCTGTTTTGCACTGTGCTTTTGTCATCTTGTTTGACGGTGTAAAATGTGTATCCATTTATATCGTATCCTTGCCATGTGTCTATGGTCCAAGACGGT[C/T]
CCATCCCCAACAACTGTACTGTCTCATTTGGGACATCCATGGACATTGTCACACGATTCTTGAACCATTCGTTGAACCGAGAATTATGTTCTCTGTTAAT
Reverse complement sequence
ATTAACAGAGAACATAATTCTCGGTTCAACGAATGGTTCAAGAATCGTGTGACAATGTCCATGGATGTCCCAAATGAGACAGTACAGTTGTTGGGGATGG[G/A]
ACCGTCTTGGACCATAGACACATGGCAAGGATACGATATAAATGGATACACATTTTACACCGTCAAACAAGATGACAAAAGCACAGTGCAAAACAGCGAC
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 | 30.60% | 10.80% | 14.96% | 43.69% | NA |
| All Indica | 2759 | 7.30% | 18.20% | 15.95% | 58.54% | NA |
| All Japonica | 1512 | 58.30% | 0.10% | 14.81% | 26.85% | NA |
| Aus | 269 | 97.00% | 0.00% | 2.60% | 0.37% | NA |
| Indica I | 595 | 2.50% | 13.40% | 10.25% | 73.78% | NA |
| Indica II | 465 | 4.10% | 34.60% | 14.19% | 47.10% | NA |
| Indica III | 913 | 8.40% | 13.10% | 19.39% | 59.04% | NA |
| Indica Intermediate | 786 | 11.50% | 18.10% | 17.30% | 53.18% | NA |
| Temperate Japonica | 767 | 70.10% | 0.10% | 23.08% | 6.65% | NA |
| Tropical Japonica | 504 | 32.10% | 0.00% | 7.54% | 60.32% | NA |
| Japonica Intermediate | 241 | 75.10% | 0.00% | 3.73% | 21.16% | NA |
| VI/Aromatic | 96 | 67.70% | 0.00% | 18.75% | 13.54% | NA |
| Intermediate | 90 | 41.10% | 5.60% | 20.00% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670943 | C -> T | LOC_Os10g14130.1 | missense_variant ; p.Gly323Glu; MODERATE | nonsynonymous_codon ; G323E | Average:12.339; most accessible tissue: Callus, score: 18.912 | probably damaging  |
2.339 |
DELETERIOUS | 0.02 |
| vg1007670943 | C -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:12.339; most accessible tissue: Callus, score: 18.912 | N | N | N | N |