Search for Variation information by Variation ID:
Detailed information for vg0139512492:
| Variant ID: vg0139512492 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39512492 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTGTCTTTAGGACAATGCTTGTAGGTGTGCCCATGTTCATTGTATTTGCTGCAACGCTTCACCCTGCCAGCCTCCGACTCGTCCATATTGTTGCGGATG[C/A]
GACGAGTCCTCCTCCTTCCAGCCTTGCCTCGGAGCTTCGATGGGTCAGGAATATTGAGTACTTCATCGTTAGTCTCTGTGAACTCCCCAGCTATGCCGAA
Reverse complement sequence
TTCGGCATAGCTGGGGAGTTCACAGAGACTAACGATGAAGTACTCAATATTCCTGACCCATCGAAGCTCCGAGGCAAGGCTGGAAGGAGGAGGACTCGTC[G/T]
CATCCGCAACAATATGGACGAGTCGGAGGCTGGCAGGGTGAAGCGTTGCAGCAAATACAATGAACATGGGCACACCTACAAGCATTGTCCTAAAGACAAG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.50% | 0.50% | 0.63% | 71.39% | NA |
| All Indica | 2759 | 3.40% | 0.80% | 0.76% | 94.96% | NA |
| All Japonica | 1512 | 74.70% | 0.00% | 0.00% | 25.26% | NA |
| Aus | 269 | 3.00% | 0.00% | 1.86% | 95.17% | NA |
| Indica I | 595 | 3.50% | 0.20% | 0.34% | 95.97% | NA |
| Indica II | 465 | 4.30% | 0.00% | 1.08% | 94.62% | NA |
| Indica III | 913 | 1.80% | 0.20% | 0.66% | 97.37% | NA |
| Indica Intermediate | 786 | 4.80% | 2.50% | 1.02% | 91.60% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.00% | 2.74% | NA |
| Tropical Japonica | 504 | 52.40% | 0.00% | 0.00% | 47.62% | NA |
| Japonica Intermediate | 241 | 49.80% | 0.00% | 0.00% | 50.21% | NA |
| VI/Aromatic | 96 | 26.00% | 0.00% | 4.17% | 69.79% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 0.00% | 54.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139512492 | C -> A | LOC_Os01g67990.1 | missense_variant ; p.Arg801Leu; MODERATE | nonsynonymous_codon ; R801L | Average:9.347; most accessible tissue: Zhenshan97 root, score: 18.731 | possibly damaging  |
1.515 |
DELETERIOUS | 0.00 |
| vg0139512492 | C -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:9.347; most accessible tissue: Zhenshan97 root, score: 18.731 | N | N | N | N |