Search for Variation information by Variation ID:
Detailed information for vg0409085097:
| Variant ID: vg0409085097 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9085097 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 89. )
Flanking Sequence (100 bp) in Reference Genome:
GGATAGATCGGTCGCCATGCCGAGACAGTATAAATCACTTAGATCGAAATATATATTAATAATTAGACTATATACGTTCATAGCATAGCCGATCACGGAG[C/A]
TCTCCTATGGCGATCCTTGCCACCTCCTGACATGCATGGATGTAGTTTCTTCCTCCAGCTTCAAACATCACTGAGGGGATATCTTCACTATTACTGTTCA
Reverse complement sequence
TGAACAGTAATAGTGAAGATATCCCCTCAGTGATGTTTGAAGCTGGAGGAAGAAACTACATCCATGCATGTCAGGAGGTGGCAAGGATCGCCATAGGAGA[G/T]
CTCCGTGATCGGCTATGCTATGAACGTATATAGTCTAATTATTAATATATATTTCGATCTAAGTGATTTATACTGTCTCGGCATGGCGACCGATCTATCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.40% | 4.50% | 1.61% | 73.49% | NA |
| All Indica | 2759 | 0.80% | 5.10% | 0.58% | 93.48% | NA |
| All Japonica | 1512 | 60.80% | 2.90% | 2.38% | 33.86% | NA |
| Aus | 269 | 0.40% | 6.70% | 0.00% | 92.94% | NA |
| Indica I | 595 | 0.30% | 3.40% | 0.50% | 95.80% | NA |
| Indica II | 465 | 1.30% | 4.90% | 0.00% | 93.76% | NA |
| Indica III | 913 | 0.40% | 7.40% | 1.20% | 90.91% | NA |
| Indica Intermediate | 786 | 1.40% | 3.80% | 0.25% | 94.53% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.13% | 4.04% | NA |
| Tropical Japonica | 504 | 4.20% | 7.50% | 5.75% | 82.54% | NA |
| Japonica Intermediate | 241 | 68.00% | 2.50% | 2.49% | 26.97% | NA |
| VI/Aromatic | 96 | 0.00% | 7.30% | 20.83% | 71.88% | NA |
| Intermediate | 90 | 22.20% | 3.30% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409085097 | C -> DEL | LOC_Os04g16700.1 | N | frameshift_variant | Average:15.787; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg0409085097 | C -> A | LOC_Os04g16700.1 | missense_variant ; p.Glu85Asp; MODERATE | nonsynonymous_codon ; E85D | Average:15.787; most accessible tissue: Minghui63 panicle, score: 25.313 | benign  |
1.186 |
DELETERIOUS | 0.04 |