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Detailed information for vg0136012677:
| Variant ID: vg0136012677 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36012677 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, T: 0.29, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
CCTGAGCACTATGCTTGTGTGGTTGATCTCTTCTCCAGGGCTAAGCGATTTGATGATGCCAAGCGGTTTCTTGAGAACCTTCCCTTCGAGCCAGGCATTG[G/T]
ATTCTGGAAGTCGTTGATAGGAGGGTGCCAGATTCACTGGAATAGGGAGCTGGCTAAGAGTGTCGCGAAGCATATTCATGCACTGGATCCTAAGGATACT
Reverse complement sequence
AGTATCCTTAGGATCCAGTGCATGAATATGCTTCGCGACACTCTTAGCCAGCTCCCTATTCCAGTGAATCTGGCACCCTCCTATCAACGACTTCCAGAAT[C/A]
CAATGCCTGGCTCGAAGGGAAGGTTCTCAAGAAACCGCTTGGCATCATCAAATCGCTTAGCCCTGGAGAAGAGATCAACCACACAAGCATAGTGCTCAGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.70% | 33.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 2.00% | 98.00% | 0.00% | 0.00% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.80% | 97.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 3.30% | 96.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 83.30% | 16.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 50.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0136012677 | G -> T | LOC_Os01g62220.1 | missense_variant ; p.Gly343Val; MODERATE | nonsynonymous_codon ; G343V | Average:73.473; most accessible tissue: Callus, score: 91.254 | benign  |
0.995 |
TOLERATED | 0.07 |