Search for Variation information by Variation ID:
Detailed information for vg0430653739:
| Variant ID: vg0430653739 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30653739 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CATGTCTTCGCAGTAGTCGCCGAAGAGTTCACTAGTGAATTGGGTGCCATTATCCGTAATGATACGGTTAGGCACTCCAAAACGGGCCGTGATGCCCTTA[A/C]
TGAATTTAAGTGCAGAGTGCTTATCGATCTTGACGACCGGATAAGCCTCGGGCCACTTAGTGAACTTGTCGATCGCGACATACAGATACTCAAACCCGCC
Reverse complement sequence
GGCGGGTTTGAGTATCTGTATGTCGCGATCGACAAGTTCACTAAGTGGCCCGAGGCTTATCCGGTCGTCAAGATCGATAAGCACTCTGCACTTAAATTCA[T/G]
TAAGGGCATCACGGCCCGTTTTGGAGTGCCTAACCGTATCATTACGGATAATGGCACCCAATTCACTAGTGAACTCTTCGGCGACTACTGCGAAGACATG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.70% | 0.80% | 1.12% | 15.36% | NA |
| All Indica | 2759 | 96.60% | 1.10% | 1.56% | 0.69% | NA |
| All Japonica | 1512 | 55.80% | 0.00% | 0.53% | 43.65% | NA |
| Aus | 269 | 91.10% | 0.70% | 0.37% | 7.81% | NA |
| Indica I | 595 | 97.30% | 0.50% | 2.02% | 0.17% | NA |
| Indica II | 465 | 97.20% | 0.90% | 1.29% | 0.65% | NA |
| Indica III | 913 | 96.60% | 2.00% | 1.31% | 0.11% | NA |
| Indica Intermediate | 786 | 95.80% | 0.80% | 1.65% | 1.78% | NA |
| Temperate Japonica | 767 | 64.90% | 0.00% | 0.39% | 34.68% | NA |
| Tropical Japonica | 504 | 46.20% | 0.00% | 0.60% | 53.17% | NA |
| Japonica Intermediate | 241 | 46.90% | 0.00% | 0.83% | 52.28% | NA |
| VI/Aromatic | 96 | 80.20% | 1.00% | 0.00% | 18.75% | NA |
| Intermediate | 90 | 86.70% | 3.30% | 1.11% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430653739 | A -> C | LOC_Os04g51730.1 | missense_variant ; p.Ile208Ser; MODERATE | nonsynonymous_codon ; I208S | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | probably damaging  |
2.075 |
DELETERIOUS | 0.00 |
| vg0430653739 | A -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |