Search for Variation information by Variation ID:
Detailed information for vg0430653703:
| Variant ID: vg0430653703 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30653703 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 345. )
Flanking Sequence (100 bp) in Reference Genome:
GGGGTGGGCAGGTGAGGCGAAGCAGAGCTTGATGCCCATGTCTTCGCAGTAGTCGCCGAAGAGTTCACTAGTGAATTGGGTGCCATTATCCGTAATGATA[C/T]
GGTTAGGCACTCCAAAACGGGCCGTGATGCCCTTAATGAATTTAAGTGCAGAGTGCTTATCGATCTTGACGACCGGATAAGCCTCGGGCCACTTAGTGAA
Reverse complement sequence
TTCACTAAGTGGCCCGAGGCTTATCCGGTCGTCAAGATCGATAAGCACTCTGCACTTAAATTCATTAAGGGCATCACGGCCCGTTTTGGAGTGCCTAACC[G/A]
TATCATTACGGATAATGGCACCCAATTCACTAGTGAACTCTTCGGCGACTACTGCGAAGACATGGGCATCAAGCTCTGCTTCGCCTCACCTGCCCACCCC
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 | 84.30% | 0.00% | 0.36% | 15.26% | NA |
| All Indica | 2759 | 99.00% | 0.10% | 0.22% | 0.69% | NA |
| All Japonica | 1512 | 56.30% | 0.00% | 0.46% | 43.25% | NA |
| Aus | 269 | 92.20% | 0.00% | 0.00% | 7.81% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 98.90% | 0.00% | 0.43% | 0.65% | NA |
| Indica III | 913 | 99.60% | 0.20% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 97.80% | 0.00% | 0.38% | 1.78% | NA |
| Temperate Japonica | 767 | 65.60% | 0.00% | 0.26% | 34.16% | NA |
| Tropical Japonica | 504 | 46.00% | 0.00% | 0.20% | 53.77% | NA |
| Japonica Intermediate | 241 | 48.10% | 0.00% | 1.66% | 50.21% | NA |
| VI/Aromatic | 96 | 78.10% | 0.00% | 3.12% | 18.75% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 1.11% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430653703 | C -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0430653703 | C -> T | LOC_Os04g51730.1 | missense_variant ; p.Arg220His; MODERATE | nonsynonymous_codon ; R220H | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
0.862 |
DELETERIOUS | 0.01 |