Search for Variation information by Variation ID:
Detailed information for vg0404363080:
| Variant ID: vg0404363080 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4363080 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )
Flanking Sequence (100 bp) in Reference Genome:
GCTACATGTTCCTTGAACACGTTGGGTGGTAGGCCTTTCGTGAGCGGATCCGCGAGCATCCTTTCTGTTTTAATGTGCTCGAGACTGATTGTTTGATCCC[G/A]
GACTTTGTCCTTCACAACATAGTACTTTATGTCAATGTGTTTGGCAGCACCACTTGACTGATTGTTGTGAGCGTACATTACTGCGGGTTCGTTGTCGCAG
Reverse complement sequence
CTGCGACAACGAACCCGCAGTAATGTACGCTCACAACAATCAGTCAAGTGGTGCTGCCAAACACATTGACATAAAGTACTATGTTGTGAAGGACAAAGTC[C/T]
GGGATCAAACAATCAGTCTCGAGCACATTAAAACAGAAAGGATGCTCGCGGATCCGCTCACGAAAGGCCTACCACCCAACGTGTTCAAGGAACATGTAGC
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 | 9.80% | 0.10% | 23.89% | 66.19% | NA |
| All Indica | 2759 | 10.00% | 0.00% | 20.95% | 69.05% | NA |
| All Japonica | 1512 | 10.80% | 0.30% | 31.55% | 57.34% | NA |
| Aus | 269 | 6.30% | 0.00% | 13.75% | 79.93% | NA |
| Indica I | 595 | 8.70% | 0.00% | 24.20% | 67.06% | NA |
| Indica II | 465 | 20.60% | 0.00% | 25.59% | 53.76% | NA |
| Indica III | 913 | 2.80% | 0.00% | 16.32% | 80.83% | NA |
| Indica Intermediate | 786 | 13.00% | 0.00% | 21.12% | 65.90% | NA |
| Temperate Japonica | 767 | 17.50% | 0.10% | 52.15% | 30.25% | NA |
| Tropical Japonica | 504 | 4.20% | 0.20% | 4.76% | 90.87% | NA |
| Japonica Intermediate | 241 | 3.30% | 1.20% | 21.99% | 73.44% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 13.54% | 86.46% | NA |
| Intermediate | 90 | 8.90% | 0.00% | 26.67% | 64.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404363080 | G -> DEL | LOC_Os04g08210.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0404363080 | G -> A | LOC_Os04g08210.1 | missense_variant ; p.Arg1364Trp; MODERATE | nonsynonymous_codon ; R1364W | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.536 |
DELETERIOUS | 0.03 |