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Detailed information for vg0420971503:
| Variant ID: vg0420971503 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20971503 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )
Flanking Sequence (100 bp) in Reference Genome:
GGACTCAGCAAGAAACGTCCATGGCATTCCTACAGCTGTTTCGGCCCATTCTGCTTCTTTGATGTGGATGGGACTGAGTCCCAACCATCTGGAAGTGGTT[C/T]
ATGGGTGAATGAGGATGAAGTGGAATTCATAACCCTCTTATATCATCAAATGGCTATGCGCTATCCAGAACTCAAATCTAGTTCCCAGGTAGCTGTCATA
Reverse complement sequence
TATGACAGCTACCTGGGAACTAGATTTGAGTTCTGGATAGCGCATAGCCATTTGATGATATAAGAGGGTTATGAATTCCACTTCATCCTCATTCACCCAT[G/A]
AACCACTTCCAGATGGTTGGGACTCAGTCCCATCCACATCAAAGAAGCAGAATGGGCCGAAACAGCTGTAGGAATGCCATGGACGTTTCTTGCTGAGTCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.10% | 0.30% | 2.75% | 38.87% | NA |
| All Indica | 2759 | 41.20% | 0.00% | 1.59% | 57.23% | NA |
| All Japonica | 1512 | 92.50% | 0.90% | 3.17% | 3.44% | NA |
| Aus | 269 | 29.00% | 0.00% | 3.72% | 67.29% | NA |
| Indica I | 595 | 77.50% | 0.00% | 0.50% | 22.02% | NA |
| Indica II | 465 | 18.10% | 0.00% | 0.86% | 81.08% | NA |
| Indica III | 913 | 35.80% | 0.00% | 2.74% | 61.45% | NA |
| Indica Intermediate | 786 | 33.60% | 0.00% | 1.53% | 64.89% | NA |
| Temperate Japonica | 767 | 99.50% | 0.30% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 83.50% | 0.00% | 8.53% | 7.94% | NA |
| Japonica Intermediate | 241 | 89.20% | 4.60% | 1.66% | 4.56% | NA |
| VI/Aromatic | 96 | 66.70% | 0.00% | 26.04% | 7.29% | NA |
| Intermediate | 90 | 75.60% | 1.10% | 3.33% | 20.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420971503 | C -> DEL | LOC_Os04g34670.1 | N | frameshift_variant | Average:8.596; most accessible tissue: Zhenshan97 flower, score: 19.853 | N | N | N | N |
| vg0420971503 | C -> T | LOC_Os04g34670.1 | missense_variant ; p.Ser552Leu; MODERATE | nonsynonymous_codon ; S552L | Average:8.596; most accessible tissue: Zhenshan97 flower, score: 19.853 | possibly damaging  |
1.896 |
DELETERIOUS | 0.00 |