Search for Variation information by Variation ID:
Detailed information for vg0142999865:
| Variant ID: vg0142999865 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42999865 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 117. )
Flanking Sequence (100 bp) in Reference Genome:
AGCGGGCAAAGGGCCAACTCCGGTCGTCAGGGGCCTTAGGCCTCCGTTCGGCTCGGGGGCCTCTTCTCCCTGCTCTTTCCCGGGTCGAGTCAGCACAGGG[T/C]
TAGCCTCGGGGTCAAAGGGCGATAGGTGCGGCCTTCCCACAGTGGCCTCAGGGCCTTCCTGGGGGTCGGGGGCTCCTAGCACCGTCTGACAAGCGGGCAG
Reverse complement sequence
CTGCCCGCTTGTCAGACGGTGCTAGGAGCCCCCGACCCCCAGGAAGGCCCTGAGGCCACTGTGGGAAGGCCGCACCTATCGCCCTTTGACCCCGAGGCTA[A/G]
CCCTGTGCTGACTCGACCCGGGAAAGAGCAGGGAGAAGAGGCCCCCGAGCCGAACGGAGGCCTAAGGCCCCTGACGACCGGAGTTGGCCCTTTGCCCGCT
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 | 9.50% | 0.20% | 11.19% | 79.09% | NA |
| All Indica | 2759 | 3.30% | 0.40% | 12.18% | 84.12% | NA |
| All Japonica | 1512 | 20.70% | 0.00% | 4.23% | 75.07% | NA |
| Aus | 269 | 10.00% | 0.00% | 34.94% | 55.02% | NA |
| Indica I | 595 | 1.50% | 0.00% | 5.55% | 92.94% | NA |
| Indica II | 465 | 2.40% | 0.00% | 5.81% | 91.83% | NA |
| Indica III | 913 | 4.70% | 0.90% | 20.37% | 74.04% | NA |
| Indica Intermediate | 786 | 3.70% | 0.30% | 11.45% | 84.61% | NA |
| Temperate Japonica | 767 | 38.60% | 0.00% | 0.52% | 60.89% | NA |
| Tropical Japonica | 504 | 1.00% | 0.00% | 10.12% | 88.89% | NA |
| Japonica Intermediate | 241 | 5.00% | 0.00% | 3.73% | 91.29% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 25.00% | 73.96% | NA |
| Intermediate | 90 | 16.70% | 1.10% | 12.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0142999865 | T -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:4.687; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0142999865 | T -> C | LOC_Os01g74230.1 | missense_variant ; p.Asn1046Ser; MODERATE | nonsynonymous_codon | Average:4.687; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign  |
0.437 |
DELETERIOUS | 0.03 |