Search for Variation information by Variation ID:
Detailed information for vg0139512435:
| Variant ID: vg0139512435 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39512435 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCGAGCTCCATCTGCTGCTGATCCTGATAGTCCTGCCTCCGCCGCACTTGGTTTCTCCTTGTCTTTAGGACAATGCTTGTAGGTGTGCCCATGTTCATTG[T/C]
ATTTGCTGCAACGCTTCACCCTGCCAGCCTCCGACTCGTCCATATTGTTGCGGATGCGACGAGTCCTCCTCCTTCCAGCCTTGCCTCGGAGCTTCGATGG
Reverse complement sequence
CCATCGAAGCTCCGAGGCAAGGCTGGAAGGAGGAGGACTCGTCGCATCCGCAACAATATGGACGAGTCGGAGGCTGGCAGGGTGAAGCGTTGCAGCAAAT[A/G]
CAATGAACATGGGCACACCTACAAGCATTGTCCTAAAGACAAGGAGAAACCAAGTGCGGCGGAGGCAGGACTATCAGGATCAGCAGCAGATGGAGCTCGC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.30% | 0.20% | 0.68% | 71.90% | NA |
| All Indica | 2759 | 2.90% | 0.30% | 1.05% | 95.76% | NA |
| All Japonica | 1512 | 74.80% | 0.00% | 0.13% | 25.07% | NA |
| Aus | 269 | 2.60% | 0.00% | 0.37% | 97.03% | NA |
| Indica I | 595 | 3.70% | 0.20% | 0.34% | 95.80% | NA |
| Indica II | 465 | 2.60% | 0.00% | 0.00% | 97.42% | NA |
| Indica III | 913 | 1.50% | 0.50% | 0.66% | 97.26% | NA |
| Indica Intermediate | 786 | 4.10% | 0.30% | 2.67% | 93.00% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.00% | 2.74% | NA |
| Tropical Japonica | 504 | 52.60% | 0.00% | 0.40% | 47.02% | NA |
| Japonica Intermediate | 241 | 49.80% | 0.00% | 0.00% | 50.21% | NA |
| VI/Aromatic | 96 | 28.10% | 0.00% | 0.00% | 71.88% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 0.00% | 52.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139512435 | T -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:7.02; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0139512435 | T -> C | LOC_Os01g67990.1 | missense_variant ; p.Tyr820Cys; MODERATE | nonsynonymous_codon ; Y820C | Average:7.02; most accessible tissue: Zhenshan97 root, score: 16.934 | probably damaging  |
-2.486 |
TOLERATED | 1.00 |