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Detailed information for vg0314254509:
| Variant ID: vg0314254509 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14254509 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 122. )
Flanking Sequence (100 bp) in Reference Genome:
AATCTGAGGACTGAGCTCTCCGATAAAGGTATAATTCTATCTTCAAAATCATATTTTTCTTTGTAATCCTTTTTTCTCCACCGATCAATAATATATTTCT[T/C]
TGGAATCTTCATAATGTTGAGGTGAAGCATAATTTTCAATATGTGGGAGCAAAGAAGGCCATCTTTCTCAAATTTTGAGCAAATACAAGTGTATTCCTCC
Reverse complement sequence
GGAGGAATACACTTGTATTTGCTCAAAATTTGAGAAAGATGGCCTTCTTTGCTCCCACATATTGAAAATTATGCTTCACCTCAACATTATGAAGATTCCA[A/G]
AGAAATATATTATTGATCGGTGGAGAAAAAAGGATTACAAAGAAAAATATGATTTTGAAGATAGAATTATACCTTTATCGGAGAGCTCAGTCCTCAGATT
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 | 32.40% | 0.50% | 2.50% | 64.66% | NA |
| All Indica | 2759 | 1.40% | 0.70% | 1.74% | 96.16% | NA |
| All Japonica | 1512 | 91.40% | 0.20% | 4.37% | 4.03% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 0.30% | 0.00% | 0.50% | 99.16% | NA |
| Indica II | 465 | 0.20% | 1.10% | 0.22% | 98.49% | NA |
| Indica III | 913 | 2.60% | 1.30% | 1.97% | 94.09% | NA |
| Indica Intermediate | 786 | 1.50% | 0.30% | 3.31% | 94.91% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.91% | 0.65% | NA |
| Tropical Japonica | 504 | 84.90% | 0.20% | 7.94% | 6.94% | NA |
| Japonica Intermediate | 241 | 82.60% | 0.80% | 7.88% | 8.71% | NA |
| VI/Aromatic | 96 | 70.80% | 1.00% | 0.00% | 28.12% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 4.44% | 52.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0314254509 | T -> C | LOC_Os03g24970.1 | missense_variant ; p.Lys126Glu; MODERATE | nonsynonymous_codon ; K126E | Average:4.462; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-0.521 |
TOLERATED | 1.00 |
| vg0314254509 | T -> DEL | LOC_Os03g24970.1 | N | frameshift_variant | Average:4.462; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |