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Detailed information for vg0428145320:
| Variant ID: vg0428145320 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 28145320 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 57. )
Flanking Sequence (100 bp) in Reference Genome:
TAGCACCATGGCTACGGGAAAGTATGCAAAGGACTCAAGTTCAGTCCTAGGAACAGAGGATGTCCAAACTGAAAATGATGAAGAGGAAAATGATGGCCCT[G/A]
CCACTACTGATGATCGTGCGGAGGTATCATCTGCAAGCAAGCCAAAGAAAGCCAGAACACAAGAAATTGAAGATGATGGGCTGATTGGTGCATTCACCAG
Reverse complement sequence
CTGGTGAATGCACCAATCAGCCCATCATCTTCAATTTCTTGTGTTCTGGCTTTCTTTGGCTTGCTTGCAGATGATACCTCCGCACGATCATCAGTAGTGG[C/T]
AGGGCCATCATTTTCCTCTTCATCATTTTCAGTTTGGACATCCTCTGTTCCTAGGACTGAACTTGAGTCCTTTGCATACTTTCCCGTAGCCATGGTGCTA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.20% | 0.10% | 29.92% | 41.75% | NA |
| All Indica | 2759 | 6.50% | 0.00% | 26.50% | 66.98% | NA |
| All Japonica | 1512 | 61.80% | 0.50% | 32.80% | 4.89% | NA |
| Aus | 269 | 44.60% | 0.00% | 45.35% | 10.04% | NA |
| Indica I | 595 | 3.20% | 0.00% | 14.45% | 82.35% | NA |
| Indica II | 465 | 3.40% | 0.00% | 41.72% | 54.84% | NA |
| Indica III | 913 | 10.00% | 0.00% | 24.42% | 65.61% | NA |
| Indica Intermediate | 786 | 6.90% | 0.00% | 29.01% | 64.12% | NA |
| Temperate Japonica | 767 | 68.30% | 0.90% | 28.29% | 2.48% | NA |
| Tropical Japonica | 504 | 53.40% | 0.00% | 38.69% | 7.94% | NA |
| Japonica Intermediate | 241 | 58.90% | 0.00% | 34.85% | 6.22% | NA |
| VI/Aromatic | 96 | 56.20% | 0.00% | 38.54% | 5.21% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 31.11% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0428145320 | G -> DEL | LOC_Os04g47440.1 | N | frameshift_variant | Average:4.723; most accessible tissue: Callus, score: 7.289 | N | N | N | N |
| vg0428145320 | G -> A | LOC_Os04g47440.1 | missense_variant ; p.Ala96Thr; MODERATE | nonsynonymous_codon ; A96T | Average:4.723; most accessible tissue: Callus, score: 7.289 | benign  |
1.211 |
TOLERATED | 0.30 |