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Detailed information for vg0719561972:
| Variant ID: vg0719561972 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19561972 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 281. )
Flanking Sequence (100 bp) in Reference Genome:
CCTATAATACCACGGCTAAGGCGTTTGTTCAGGAACAAGGGGAATGCTAGAATGTTGCGATGGCACGCTGAAGAGCGTCAACAGGACGGGATGCTGAGAC[A/C]
CCCCGCCGATGGTTCGCAGTGGCGAAACATCGACAGAAAATTTAAAGAATTTGGAAAGGACGCACGAAACATACGGTTTGGTTTGAGTACGGATGGCATG
Reverse complement sequence
CATGCCATCCGTACTCAAACCAAACCGTATGTTTCGTGCGTCCTTTCCAAATTCTTTAAATTTTCTGTCGATGTTTCGCCACTGCGAACCATCGGCGGGG[T/G]
GTCTCAGCATCCCGTCCTGTTGACGCTCTTCAGCGTGCCATCGCAACATTCTAGCATTCCCCTTGTTCCTGAACAAACGCCTTAGCCGTGGTATTATAGG
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 | 22.20% | 0.10% | 26.77% | 50.99% | NA |
| All Indica | 2759 | 3.60% | 0.00% | 25.37% | 71.04% | NA |
| All Japonica | 1512 | 60.50% | 0.20% | 24.74% | 14.55% | NA |
| Aus | 269 | 7.10% | 0.00% | 59.11% | 33.83% | NA |
| Indica I | 595 | 1.50% | 0.00% | 6.05% | 92.44% | NA |
| Indica II | 465 | 3.20% | 0.00% | 23.87% | 72.90% | NA |
| Indica III | 913 | 4.50% | 0.00% | 42.61% | 52.90% | NA |
| Indica Intermediate | 786 | 4.20% | 0.10% | 20.87% | 74.81% | NA |
| Temperate Japonica | 767 | 93.20% | 0.30% | 3.52% | 3.00% | NA |
| Tropical Japonica | 504 | 12.30% | 0.20% | 56.55% | 30.95% | NA |
| Japonica Intermediate | 241 | 57.30% | 0.00% | 25.73% | 17.01% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 5.21% | 94.79% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 30.00% | 53.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719561972 | A -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:5.421; most accessible tissue: Callus, score: 10.667 | N | N | N | N |
| vg0719561972 | A -> C | LOC_Os07g32740.1 | missense_variant ; p.His310Pro; MODERATE | nonsynonymous_codon ; H310P | Average:5.421; most accessible tissue: Callus, score: 10.667 | probably damaging  |
2.526 |
DELETERIOUS | 0.00 |