Search for Variation information by Variation ID:
Detailed information for vg1101255550:
| Variant ID: vg1101255550 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1255550 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
GCCAAACTCAAGGAGAACCAAAAAATTAAAGTTGAGTTTTACAACAATCGTGCTCTTTCGAATAGTTTTTCACGTCATCTGGGTAGAATTGTTCGTGATC[G/A]
GAACATTACTCCGGTCAAAGTGAAGAAATGGTCAGACATTAGTAACACAGAGCAGGAACACATATTTGCCTCGATTACGGTACGCATCTATCTTCCTATG
Reverse complement sequence
CATAGGAAGATAGATGCGTACCGTAATCGAGGCAAATATGTGTTCCTGCTCTGTGTTACTAATGTCTGACCATTTCTTCACTTTGACCGGAGTAATGTTC[C/T]
GATCACGAACAATTCTACCCAGATGACGTGAAAAACTATTCGAAAGAGCACGATTGTTGTAAAACTCAACTTTAATTTTTTGGTTCTCCTTGAGTTTGGC
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 | 67.70% | 0.50% | 3.07% | 28.76% | NA |
| All Indica | 2759 | 51.10% | 0.80% | 4.10% | 44.04% | NA |
| All Japonica | 1512 | 97.60% | 0.00% | 0.33% | 2.05% | NA |
| Aus | 269 | 71.00% | 1.10% | 7.06% | 20.82% | NA |
| Indica I | 595 | 16.60% | 0.00% | 9.92% | 73.45% | NA |
| Indica II | 465 | 50.30% | 1.10% | 2.15% | 46.45% | NA |
| Indica III | 913 | 70.60% | 1.00% | 1.75% | 26.62% | NA |
| Indica Intermediate | 786 | 55.00% | 0.90% | 3.56% | 40.59% | NA |
| Temperate Japonica | 767 | 97.90% | 0.00% | 0.65% | 1.43% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 0.00% | 2.18% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 63.50% | 0.00% | 2.08% | 34.38% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 6.67% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101255550 | G -> A | LOC_Os11g03340.1 | missense_variant ; p.Arg160Gln; MODERATE | nonsynonymous_codon ; R160Q | Average:6.578; most accessible tissue: Minghui63 flag leaf, score: 11.122 | benign  |
1.318 |
TOLERATED | 0.09 |
| vg1101255550 | G -> DEL | LOC_Os11g03340.1 | N | frameshift_variant | Average:6.578; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |