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Detailed information for vg0233336536:
| Variant ID: vg0233336536 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 33336536 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 126. )
Flanking Sequence (100 bp) in Reference Genome:
GACCGATGTGCGGCCATGCGTTCATCAACCTTCCTTGCCACCTCCTCTTGCATGTTGAGTTCGTAGCTCGATACCCGGAACTCTAGGTCTGCAATCTTCG[C/T]
CTCGGTATCTCTCTTGCTCCTCATCCGACTCCTGTACGTGTGGATGTCCTCCTTAAAACCAATCTTCCAAGGAATCACCCCTTTCCCTCGAGTTCGTCCT
Reverse complement sequence
AGGACGAACTCGAGGGAAAGGGGTGATTCCTTGGAAGATTGGTTTTAAGGAGGACATCCACACGTACAGGAGTCGGATGAGGAGCAAGAGAGATACCGAG[G/A]
CGAAGATTGCAGACCTAGAGTTCCGGGTATCGAGCTACGAACTCAACATGCAAGAGGAGGTGGCAAGGAAGGTTGATGAACGCATGGCCGCACATCGGTC
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 | 35.70% | 1.40% | 5.69% | 57.24% | NA |
| All Indica | 2759 | 2.20% | 2.00% | 5.80% | 89.96% | NA |
| All Japonica | 1512 | 97.60% | 0.10% | 1.59% | 0.73% | NA |
| Aus | 269 | 4.10% | 2.60% | 29.00% | 64.31% | NA |
| Indica I | 595 | 1.50% | 0.00% | 5.21% | 93.28% | NA |
| Indica II | 465 | 2.80% | 5.40% | 3.01% | 88.82% | NA |
| Indica III | 913 | 1.20% | 1.30% | 5.48% | 92.00% | NA |
| Indica Intermediate | 786 | 3.70% | 2.30% | 8.27% | 85.75% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.39% | 0.78% | NA |
| Tropical Japonica | 504 | 95.80% | 0.40% | 3.77% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.83% | 2.07% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 0.00% | 10.42% | NA |
| Intermediate | 90 | 56.70% | 3.30% | 7.78% | 32.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0233336536 | C -> T | LOC_Os02g54400.1 | missense_variant ; p.Ala273Thr; MODERATE | nonsynonymous_codon ; A273T | Average:4.518; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.719 |
DELETERIOUS | 0.03 |
| vg0233336536 | C -> DEL | LOC_Os02g54400.1 | N | frameshift_variant | Average:4.518; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |