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Detailed information for vg1101255544:
| Variant ID: vg1101255544 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1255544 |
| 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, A: 0.00, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
GAAGTTGCCAAACTCAAGGAGAACCAAAAAATTAAAGTTGAGTTTTACAACAATCGTGCTCTTTCGAATAGTTTTTCACGTCATCTGGGTAGAATTGTTC[G/A]
TGATCGGAACATTACTCCGGTCAAAGTGAAGAAATGGTCAGACATTAGTAACACAGAGCAGGAACACATATTTGCCTCGATTACGGTACGCATCTATCTT
Reverse complement sequence
AAGATAGATGCGTACCGTAATCGAGGCAAATATGTGTTCCTGCTCTGTGTTACTAATGTCTGACCATTTCTTCACTTTGACCGGAGTAATGTTCCGATCA[C/T]
GAACAATTCTACCCAGATGACGTGAAAAACTATTCGAAAGAGCACGATTGTTGTAAAACTCAACTTTAATTTTTTGGTTCTCCTTGAGTTTGGCAACTTC
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 | 36.60% | 0.40% | 26.56% | 36.50% | NA |
| All Indica | 2759 | 5.50% | 0.70% | 37.95% | 55.89% | NA |
| All Japonica | 1512 | 97.10% | 0.00% | 0.33% | 2.58% | NA |
| Aus | 269 | 13.00% | 0.00% | 63.20% | 23.79% | NA |
| Indica I | 595 | 4.00% | 0.00% | 8.24% | 87.73% | NA |
| Indica II | 465 | 5.80% | 0.60% | 30.54% | 63.01% | NA |
| Indica III | 913 | 3.10% | 1.20% | 62.54% | 33.19% | NA |
| Indica Intermediate | 786 | 9.30% | 0.50% | 36.26% | 53.94% | NA |
| Temperate Japonica | 767 | 97.50% | 0.00% | 0.26% | 2.22% | NA |
| Tropical Japonica | 504 | 97.20% | 0.00% | 0.20% | 2.58% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 0.83% | 3.73% | NA |
| VI/Aromatic | 96 | 30.20% | 0.00% | 23.96% | 45.83% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 11.11% | 40.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101255544 | G -> A | LOC_Os11g03340.1 | missense_variant ; p.Arg158His; MODERATE | nonsynonymous_codon ; R158H | Average:6.578; most accessible tissue: Minghui63 flag leaf, score: 11.122 | probably damaging  |
2.33 |
TOLERATED | 0.06 |
| vg1101255544 | G -> DEL | LOC_Os11g03340.1 | N | frameshift_variant | Average:6.578; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |