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Detailed information for vg0334133366:
| Variant ID: vg0334133366 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34133366 |
| 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: 390. )
Flanking Sequence (100 bp) in Reference Genome:
ATACCACGGCTAAGGCGTTTGTTCAGGAACAAGGGGAATGCTAGAATGTTGCGATGGCATGCTGAAGAGCGTCAACAGGACGGGATGCTGAGACACCCCG[C/T]
CGATGGTTCGCAATGGCGAAACATCGACAGAAAATTTAAAGAATTTGGAAAGGACGCACGAAACATACGGTTTGGTTTGAGTACGGATGGCATGAATCCT
Reverse complement sequence
AGGATTCATGCCATCCGTACTCAAACCAAACCGTATGTTTCGTGCGTCCTTTCCAAATTCTTTAAATTTTCTGTCGATGTTTCGCCATTGCGAACCATCG[G/A]
CGGGGTGTCTCAGCATCCCGTCCTGTTGACGCTCTTCAGCATGCCATCGCAACATTCTAGCATTCCCCTTGTTCCTGAACAAACGCCTTAGCCGTGGTAT
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 | 21.80% | 0.70% | 8.89% | 68.66% | NA |
| All Indica | 2759 | 35.50% | 0.20% | 13.88% | 50.42% | NA |
| All Japonica | 1512 | 0.50% | 1.20% | 1.39% | 96.89% | NA |
| Aus | 269 | 8.20% | 0.00% | 2.23% | 89.59% | NA |
| Indica I | 595 | 9.40% | 0.20% | 6.89% | 83.53% | NA |
| Indica II | 465 | 41.30% | 0.20% | 13.55% | 44.95% | NA |
| Indica III | 913 | 50.90% | 0.20% | 14.46% | 34.39% | NA |
| Indica Intermediate | 786 | 33.80% | 0.30% | 18.70% | 47.20% | NA |
| Temperate Japonica | 767 | 0.50% | 0.40% | 0.26% | 98.83% | NA |
| Tropical Japonica | 504 | 0.20% | 2.60% | 2.98% | 94.25% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.80% | 1.66% | 96.27% | NA |
| VI/Aromatic | 96 | 3.10% | 6.20% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 18.90% | 2.20% | 8.89% | 70.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334133366 | C -> T | LOC_Os03g60010.1 | missense_variant ; p.Ala312Val; MODERATE | nonsynonymous_codon ; A312V | Average:4.72; most accessible tissue: Minghui63 flower, score: 9.27 | benign  |
0.952 |
DELETERIOUS | 0.04 |
| vg0334133366 | C -> DEL | LOC_Os03g60010.1 | N | frameshift_variant | Average:4.72; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |