Search for Variation information by Variation ID:
Detailed information for vg0136520357:
| Variant ID: vg0136520357 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36520357 |
| 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: 318. )
Flanking Sequence (100 bp) in Reference Genome:
AGGTGTGAAAAGTTTGGTATCTCAAATATTTCGCACAATATTTGTTTCTTCCCATCCAATTCATCTTGAGAGCAAGGGATAATAGGTTGACCTGAGCATG[G/A]
CAAGCCAAAAACTGCATTCACATCATTAGGACCGAATGGCAACTCCTGGTTGACATCTTTAACAATAGCGCATGATTTCGGATCAACTTTGCTCAGTAGC
Reverse complement sequence
GCTACTGAGCAAAGTTGATCCGAAATCATGCGCTATTGTTAAAGATGTCAACCAGGAGTTGCCATTCGGTCCTAATGATGTGAATGCAGTTTTTGGCTTG[C/T]
CATGCTCAGGTCAACCTATTATCCCTTGCTCTCAAGATGAATTGGATGGGAAGAAACAAATATTGTGCGAAATATTTGAGATACCAAACTTTTCACACCT
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 | 34.20% | 1.30% | 4.13% | 60.33% | NA |
| All Indica | 2759 | 3.00% | 0.00% | 1.88% | 95.11% | NA |
| All Japonica | 1512 | 91.90% | 3.80% | 1.65% | 2.65% | NA |
| Aus | 269 | 0.40% | 0.00% | 42.75% | 56.88% | NA |
| Indica I | 595 | 1.20% | 0.00% | 2.52% | 96.30% | NA |
| Indica II | 465 | 3.00% | 0.00% | 0.22% | 96.77% | NA |
| Indica III | 913 | 1.50% | 0.00% | 1.10% | 97.37% | NA |
| Indica Intermediate | 786 | 6.10% | 0.00% | 3.31% | 90.59% | NA |
| Temperate Japonica | 767 | 98.40% | 0.10% | 0.26% | 1.17% | NA |
| Tropical Japonica | 504 | 83.30% | 9.70% | 3.97% | 2.98% | NA |
| Japonica Intermediate | 241 | 88.80% | 3.30% | 1.24% | 6.64% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 62.20% | 4.40% | 2.22% | 31.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136520357 | G -> A | LOC_Os01g63040.1 | missense_variant ; p.Pro178Ser; MODERATE | nonsynonymous_codon ; P178S | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.531 |
DELETERIOUS | 0.00 |
| vg0136520357 | G -> DEL | LOC_Os01g63040.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |