Search for Variation information by Variation ID:
Detailed information for vg0125111832:
| Variant ID: vg0125111832 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25111832 |
| 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: 104. )
Flanking Sequence (100 bp) in Reference Genome:
ACAGGCGGCCTGTCACACGCCTCGCCCCGTCCCATCGAAATGATGAGAGCCTCCATGCTCTCGTCCCTAGCCGGAGCCGGCGTGTTAACTCCTGGAGTTG[G/A]
CACGTCAGTCCCGGCCAGATACATTCCAGGCTTCATCGCAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTGCGGCGTGCTAAACTGACAC
Reverse complement sequence
GTGTCAGTTTAGCACGCCGCACGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTGCGATGAAGCCTGGAATGTATCTGGCCGGGACTGACGTG[C/T]
CAACTCCAGGAGTTAACACGCCGGCTCCGGCTAGGGACGAGAGCATGGAGGCTCTCATCATTTCGATGGGACGGGGCGAGGCGTGTGACAGGCCGCCTGT
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 | 7.50% | 0.60% | 14.35% | 77.57% | NA |
| All Indica | 2759 | 1.20% | 1.00% | 10.69% | 87.13% | NA |
| All Japonica | 1512 | 20.10% | 0.00% | 23.21% | 56.68% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.37% | 98.88% | NA |
| Indica I | 595 | 0.50% | 0.70% | 5.71% | 93.11% | NA |
| Indica II | 465 | 2.20% | 1.90% | 14.62% | 81.29% | NA |
| Indica III | 913 | 0.80% | 1.00% | 11.06% | 87.19% | NA |
| Indica Intermediate | 786 | 1.70% | 0.60% | 11.70% | 86.01% | NA |
| Temperate Japonica | 767 | 30.90% | 0.00% | 38.20% | 30.90% | NA |
| Tropical Japonica | 504 | 4.00% | 0.00% | 3.77% | 92.26% | NA |
| Japonica Intermediate | 241 | 19.50% | 0.00% | 16.18% | 64.32% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 12.50% | 83.33% | NA |
| Intermediate | 90 | 13.30% | 0.00% | 21.11% | 65.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0125111832 | G -> A | LOC_Os01g43830.1 | missense_variant ; p.Pro73Ser; MODERATE | nonsynonymous_codon ; P73S | Average:15.191; most accessible tissue: Minghui63 panicle, score: 38.588 | possibly damaging  |
1.739 |
DELETERIOUS | 0.00 |
| vg0125111832 | G -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:15.191; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |