Search for Variation information by Variation ID:
Detailed information for vg0719562781:
| Variant ID: vg0719562781 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562781 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 381. )
Flanking Sequence (100 bp) in Reference Genome:
TTTTGGGAGTTACCATATTGGGAATTCTTGGACGTACGCCACGCAATCGACGTGATGCACCTCACTAAGAACCTTTGCGTAAACCTTCTTGGCTTCCTAG[G/A]
TGTATACGGAAAGTCGAAAGATACACTGGAAGCACGTAATGATCTGAAGCATATGGAACAACGCGGCGACCTTCACCCGGAACCAAAGGAGAAAGGAAGC
Reverse complement sequence
GCTTCCTTTCTCCTTTGGTTCCGGGTGAAGGTCGCCGCGTTGTTCCATATGCTTCAGATCATTACGTGCTTCCAGTGTATCTTTCGACTTTCCGTATACA[C/T]
CTAGGAAGCCAAGAAGGTTTACGCAAAGGTTCTTAGTGAGGTGCATCACGTCGATTGCGTGGCGTACGTCCAAGAATTCCCAATATGGTAACTCCCAAAA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 22.40% | 0.30% | 23.47% | 53.81% | NA |
| All Indica | 2759 | 1.70% | 0.00% | 17.54% | 80.72% | NA |
| All Japonica | 1512 | 65.60% | 0.90% | 28.17% | 5.36% | NA |
| Aus | 269 | 0.40% | 0.00% | 49.44% | 50.19% | NA |
| Indica I | 595 | 0.30% | 0.00% | 4.71% | 94.96% | NA |
| Indica II | 465 | 3.70% | 0.00% | 9.68% | 86.67% | NA |
| Indica III | 913 | 1.10% | 0.00% | 30.78% | 68.13% | NA |
| Indica Intermediate | 786 | 2.40% | 0.00% | 16.54% | 81.04% | NA |
| Temperate Japonica | 767 | 93.10% | 0.40% | 4.82% | 1.69% | NA |
| Tropical Japonica | 504 | 29.80% | 1.20% | 59.92% | 9.13% | NA |
| Japonica Intermediate | 241 | 53.10% | 1.70% | 36.10% | 9.13% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 43.75% | 51.04% | NA |
| Intermediate | 90 | 15.60% | 1.10% | 26.67% | 56.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562781 | G -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.73; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0719562781 | G -> A | LOC_Os07g32740.1 | missense_variant ; p.Gly533Asp; MODERATE | nonsynonymous_codon ; G533D | Average:4.73; most accessible tissue: Zhenshan97 root, score: 10.511 | probably damaging  |
2.385 |
DELETERIOUS | 0.03 |