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Detailed information for vg0414146616:
| Variant ID: vg0414146616 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14146616 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 213. )
Flanking Sequence (100 bp) in Reference Genome:
TCGCCGAACCAGGTCGACCGCGTCATTGAGGGCAGTCGGCCAATAGAATCCTTGACGAAAGGCCTTGCCAACCAGGGTGCGCGAGGCAGAATGGGCTCCG[C/T]
ACTCGCCTTCATGGATATCGGCAAGAAGCTCAACGCCTTGTTCCCGAGGAATGCACTTCAGGAGGATTCCGTTAGCCGCGCGCCGATAGAGGATCCCTTC
Reverse complement sequence
GAAGGGATCCTCTATCGGCGCGCGGCTAACGGAATCCTCCTGAAGTGCATTCCTCGGGAACAAGGCGTTGAGCTTCTTGCCGATATCCATGAAGGCGAGT[G/A]
CGGAGCCCATTCTGCCTCGCGCACCCTGGTTGGCAAGGCCTTTCGTCAAGGATTCTATTGGCCGACTGCCCTCAATGACGCGGTCGACCTGGTTCGGCGA
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 | 0.30% | 0.20% | 14.35% | 85.21% | NA |
| All Indica | 2759 | 0.00% | 0.10% | 2.86% | 97.06% | NA |
| All Japonica | 1512 | 0.00% | 0.40% | 38.43% | 61.18% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.37% | 99.63% | NA |
| Indica I | 595 | 0.00% | 0.00% | 5.71% | 94.29% | NA |
| Indica II | 465 | 0.00% | 0.00% | 1.08% | 98.92% | NA |
| Indica III | 913 | 0.00% | 0.20% | 1.86% | 97.92% | NA |
| Indica Intermediate | 786 | 0.00% | 0.00% | 2.93% | 97.07% | NA |
| Temperate Japonica | 767 | 0.00% | 0.50% | 25.95% | 73.53% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 60.32% | 39.68% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.80% | 32.37% | 66.80% | NA |
| VI/Aromatic | 96 | 12.50% | 0.00% | 8.33% | 79.17% | NA |
| Intermediate | 90 | 0.00% | 1.10% | 10.00% | 88.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0414146616 | C -> DEL | LOC_Os04g24640.1 | N | frameshift_variant | Average:4.779; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | N | N | N | N |
| vg0414146616 | C -> T | LOC_Os04g24640.1 | missense_variant ; p.Cys163Tyr; MODERATE | nonsynonymous_codon ; C163Y | Average:4.779; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | benign  |
0.5 |
DELETERIOUS | 0.01 |