Search for Variation information by Variation ID:
Detailed information for vg0500376792:
| Variant ID: vg0500376792 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 376792 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 345. )
Flanking Sequence (100 bp) in Reference Genome:
AGAAGCATACACATTGCACAGCAGGGCATAGTGAACACTATTGTTTGGTTCCAACTCAATCAACCTCAGGACTATCCGCTCCCCCAGTTCCCACTCCCCT[C/T]
GGAACCGGCACAACCCAAGCAAACCACCCAATGCATGTGCCTTCAACTCCTCTGGCATACTCGTTAAGAGACCCTCAGCTTCTTCCAGAAGCCCAACACT
Reverse complement sequence
AGTGTTGGGCTTCTGGAAGAAGCTGAGGGTCTCTTAACGAGTATGCCAGAGGAGTTGAAGGCACATGCATTGGGTGGTTTGCTTGGGTTGTGCCGGTTCC[G/A]
AGGGGAGTGGGAACTGGGGGAGCGGATAGTCCTGAGGTTGATTGAGTTGGAACCAAACAATAGTGTTCACTATGCCCTGCTGTGCAATGTGTATGCTTCT
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 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 59.10% | 40.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0500376792 | C -> T | LOC_Os05g01635.1 | missense_variant ; p.Arg447Gln; MODERATE | nonsynonymous_codon ; R447Q | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.606 |
TOLERATED | 0.27 |