Search for Variation information by Variation ID:
Detailed information for vg0409515262:
| Variant ID: vg0409515262 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515262 |
| 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: 291. )
Flanking Sequence (100 bp) in Reference Genome:
ATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCGA[G/A]
TTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTCCGAAAAATCCTTAGGCACTACTTTCTTGTTATAATGCCTAGCAACTCGTTCCTTATCTCT
Reverse complement sequence
AGAGATAAGGAACGAGTTGCTAGGCATTATAACAAGAAAGTAGTGCCTAAGGATTTTTCGGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAA[C/T]
TCGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGAT
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 | 91.40% | 0.00% | 0.19% | 8.40% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 74.50% | 0.00% | 0.60% | 24.93% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 34.30% | 0.00% | 1.39% | 64.29% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.83% | 17.43% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 0.00% | 19.79% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515262 | G -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:31.463; most accessible tissue: Minghui63 young leaf, score: 50.756 | N | N | N | N |
| vg0409515262 | G -> A | LOC_Os04g17380.1 | missense_variant ; p.Thr115Ile; MODERATE | nonsynonymous_codon ; T115I | Average:31.463; most accessible tissue: Minghui63 young leaf, score: 50.756 | probably damaging  |
2.169 |
TOLERATED | 0.10 |