Search for Variation information by Variation ID:
Detailed information for vg0719561623:
| Variant ID: vg0719561623 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19561623 |
| 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: 313. )
Flanking Sequence (100 bp) in Reference Genome:
AAAGTTGGATACCACTCTGGAGTTGTTGCAATGGAAGGCAAAAAATGGGGTTAGTGACAAGACATTTGGCGATTTATTGAAACTCATCAAGAACATTCTT[C/A]
CGGGGGGAAACAAATTGCCCGAGACAACGTACGAGGCTAAGAAGATAGTCTGCCCGTTAGGACTGGAAGTTCATAAGATTCACGCATGTCCGAACGATTG
Reverse complement sequence
CAATCGTTCGGACATGCGTGAATCTTATGAACTTCCAGTCCTAACGGGCAGACTATCTTCTTAGCCTCGTACGTTGTCTCGGGCAATTTGTTTCCCCCCG[G/T]
AAGAATGTTCTTGATGAGTTTCAATAAATCGCCAAATGTCTTGTCACTAACCCCATTTTTTGCCTTCCATTGCAACAACTCCAGAGTGGTATCCAACTTT
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 | 5.40% | 0.40% | 42.47% | 51.69% | NA |
| All Indica | 2759 | 3.30% | 0.40% | 24.79% | 71.51% | NA |
| All Japonica | 1512 | 3.80% | 0.00% | 74.67% | 21.56% | NA |
| Aus | 269 | 37.50% | 1.90% | 57.99% | 2.60% | NA |
| Indica I | 595 | 0.50% | 0.00% | 5.04% | 94.45% | NA |
| Indica II | 465 | 1.30% | 0.00% | 23.44% | 75.27% | NA |
| Indica III | 913 | 5.10% | 1.10% | 42.28% | 51.48% | NA |
| Indica Intermediate | 786 | 4.30% | 0.30% | 20.23% | 75.19% | NA |
| Temperate Japonica | 767 | 6.00% | 0.00% | 82.79% | 11.21% | NA |
| Tropical Japonica | 504 | 0.80% | 0.00% | 66.67% | 32.54% | NA |
| Japonica Intermediate | 241 | 2.90% | 0.00% | 65.56% | 31.54% | NA |
| VI/Aromatic | 96 | 4.20% | 1.00% | 6.25% | 88.54% | NA |
| Intermediate | 90 | 4.40% | 2.20% | 35.56% | 57.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719561623 | C -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0719561623 | C -> A | LOC_Os07g32740.1 | missense_variant ; p.Pro194Thr; MODERATE | nonsynonymous_codon ; P194T | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.787 |
DELETERIOUS | 0.00 |