Search for Variation information by Variation ID:
Detailed information for vg0137648052:
| Variant ID: vg0137648052 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37648052 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAGCGCGGCATCCTCGTCTCGGCCTCAGCTGGCAACGACGGCCCGAGGCTTGGCACCCTGCACAACGGCATCCCGTGGCTTCTCACCGTCGCCGCCGGCA[T/C]
GGTGGACCGGCAAATGTTCGCCGGATCCATCTACCTCGGCGACGACACGCGGAGCACCATCACCGGCATCACGAGGTATCCAGAGAACGCGTGGATAAAG
Reverse complement sequence
CTTTATCCACGCGTTCTCTGGATACCTCGTGATGCCGGTGATGGTGCTCCGCGTGTCGTCGCCGAGGTAGATGGATCCGGCGAACATTTGCCGGTCCACC[A/G]
TGCCGGCGGCGACGGTGAGAAGCCACGGGATGCCGTTGTGCAGGGTGCCAAGCCTCGGGCCGTCGTTGCCAGCTGAGGCCGAGACGAGGATGCCGCGCTC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.40% | 35.50% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 98.20% | 1.70% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.90% | 5.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.60% | 97.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 37.80% | 60.00% | 2.22% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137648052 | T -> C | LOC_Os01g64850.1 | missense_variant ; p.Met345Thr; MODERATE | nonsynonymous_codon ; M345T | Average:80.476; most accessible tissue: Zhenshan97 flag leaf, score: 87.567 | probably damaging  |
-2.771 |
TOLERATED | 1.00 |