Search for Variation information by Variation ID:
Detailed information for vg0727004024:
| Variant ID: vg0727004024 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 27004024 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, C: 0.25, others allele: 0.00, population size: 313. )
Flanking Sequence (100 bp) in Reference Genome:
TCAGAAGAAGGTTGTTGTTCAATTAACATCGGAGTATACCCGCATCAGTAGGGATCATGCACGCGAGCTCACGAAACGCGCTGAATGTTCCTGCAACAAG[T/C]
CAAAGCTGCTTCATAAGCCCTGTTCTCATGTCATTGCCGTCTGTTGTCAGATTGGAGTTACCACTGCTGATTACATGTCCCCGTACTACACCCTGCCCTA
Reverse complement sequence
TAGGGCAGGGTGTAGTACGGGGACATGTAATCAGCAGTGGTAACTCCAATCTGACAACAGACGGCAATGACATGAGAACAGGGCTTATGAAGCAGCTTTG[A/G]
CTTGTTGCAGGAACATTCAGCGCGTTTCGTGAGCTCGCGTGCATGATCCCTACTGATGCGGGTATACTCCGATGTTAATTGAACAACAACCTTCTTCTGA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.40% | 1.50% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 99.00% | 0.90% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.30% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.50% | 7.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0727004024 | T -> C | LOC_Os07g45250.1 | missense_variant ; p.Ser654Pro; MODERATE | nonsynonymous_codon ; S654P | Average:59.437; most accessible tissue: Callus, score: 83.754 | possibly damaging  |
-1.531 |
TOLERATED | 1.00 |