Search for Variation information by Variation ID:
Detailed information for vg1209004550:
| Variant ID: vg1209004550 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004550 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACCAACCAACCGTGTAGGCGAGGACACTAGTTGACAGTGGACGAGGCGGCCGGTCAGTGAAGACGATGATGTCCATCAGCAGCGGCGCAATATGCCAGC[C/T]
GTGAAGGCGAAGAGGCTTGTCGACGGAAGATGAGGCAGCTGGCAGTGTAGAATATGTCATTATCAGCCATGGCGATAAAGACAACATGTTTGGATAAATC
Reverse complement sequence
GATTTATCCAAACATGTTGTCTTTATCGCCATGGCTGATAATGACATATTCTACACTGCCAGCTGCCTCATCTTCCGTCGACAAGCCTCTTCGCCTTCAC[G/A]
GCTGGCATATTGCGCCGCTGCTGATGGACATCATCGTCTTCACTGACCGGCCGCCTCGTCCACTGTCAACTAGTGTCCTCGCCTACACGGTTGGTTGGTC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.60% | 0.20% | 0.47% | 20.74% | NA |
| All Indica | 2759 | 65.60% | 0.30% | 0.72% | 33.38% | NA |
| All Japonica | 1512 | 99.00% | 0.00% | 0.07% | 0.93% | NA |
| Aus | 269 | 87.40% | 0.00% | 0.37% | 12.27% | NA |
| Indica I | 595 | 59.00% | 0.00% | 0.84% | 40.17% | NA |
| Indica II | 465 | 65.80% | 0.90% | 0.86% | 32.47% | NA |
| Indica III | 913 | 67.80% | 0.00% | 0.66% | 31.54% | NA |
| Indica Intermediate | 786 | 67.90% | 0.50% | 0.64% | 30.92% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004550 | C -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:46.249; most accessible tissue: Callus, score: 82.589 | N | N | N | N |
| vg1209004550 | C -> T | LOC_Os12g15770.1 | missense_variant ; p.Gly30Ser; MODERATE | nonsynonymous_codon ; G30S | Average:46.249; most accessible tissue: Callus, score: 82.589 | benign  |
0.642 |
DELETERIOUS | 0.04 |