Search for Variation information by Variation ID:
Detailed information for vg1209004514:
| Variant ID: vg1209004514 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004514 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCGATGAAGGTGTAGATGCCCAACAACGGTGGTGTGACCAACCAACCGTGTAGGCGAGGACACTAGTTGACAGTGGACGAGGCGGCCGGTCAGTGAAGA[C/T]
GATGATGTCCATCAGCAGCGGCGCAATATGCCAGCCGTGAAGGCGAAGAGGCTTGTCGACGGAAGATGAGGCAGCTGGCAGTGTAGAATATGTCATTATC
Reverse complement sequence
GATAATGACATATTCTACACTGCCAGCTGCCTCATCTTCCGTCGACAAGCCTCTTCGCCTTCACGGCTGGCATATTGCGCCGCTGCTGATGGACATCATC[G/A]
TCTTCACTGACCGGCCGCCTCGTCCACTGTCAACTAGTGTCCTCGCCTACACGGTTGGTTGGTCACACCACCGTTGTTGGGCATCTACACCTTCATCGCT
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 | 77.70% | 1.10% | 0.44% | 20.69% | NA |
| All Indica | 2759 | 64.20% | 1.80% | 0.69% | 33.31% | NA |
| All Japonica | 1512 | 99.00% | 0.10% | 0.00% | 0.93% | NA |
| Aus | 269 | 87.40% | 0.00% | 0.37% | 12.27% | NA |
| Indica I | 595 | 58.80% | 0.00% | 1.01% | 40.17% | NA |
| Indica II | 465 | 66.50% | 0.40% | 0.43% | 32.69% | NA |
| Indica III | 913 | 66.40% | 2.00% | 0.33% | 31.33% | NA |
| Indica Intermediate | 786 | 64.40% | 3.80% | 1.02% | 30.79% | NA |
| Temperate Japonica | 767 | 99.10% | 0.10% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | 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 | 87.80% | 2.20% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004514 | C -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:44.872; most accessible tissue: Callus, score: 82.589 | N | N | N | N |
| vg1209004514 | C -> T | LOC_Os12g15770.1 | missense_variant ; p.Val42Ile; MODERATE | nonsynonymous_codon ; V42I | Average:44.872; most accessible tissue: Callus, score: 82.589 | benign  |
0.344 |
TOLERATED | 0.44 |