Search for Variation information by Variation ID:
Detailed information for vg0607439497:
| Variant ID: vg0607439497 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7439497 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CACTATTATGCAACCTTAGGTGGGTATCAAGCCCATTTCCCTCGATGCACTGTCTATCACATTACGTGGTAGCCCCTTGGTAAACTGATCTGCTAGATTT[C/T]
TAGCCGTTTGGACATAGTCCAATGCTATCACTCCGGAGTTTTTCTGCTTTCTGACAGATTTCAGTCTTCTCTTGATGTGTCTAGATGACTTCATGTTGTC
Reverse complement sequence
GACAACATGAAGTCATCTAGACACATCAAGAGAAGACTGAAATCTGTCAGAAAGCAGAAAAACTCCGGAGTGATAGCATTGGACTATGTCCAAACGGCTA[G/A]
AAATCTAGCAGATCAGTTTACCAAGGGGCTACCACGTAATGTGATAGACAGTGCATCGAGGGAAATGGGCTTGATACCCACCTAAGGTTGCATAATAGTG
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 | 2.90% | 0.10% | 2.45% | 94.56% | NA |
| All Indica | 2759 | 2.20% | 0.10% | 0.98% | 96.70% | NA |
| All Japonica | 1512 | 4.50% | 0.10% | 0.53% | 94.91% | NA |
| Aus | 269 | 1.50% | 0.40% | 1.86% | 96.28% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.84% | 98.99% | NA |
| Indica II | 465 | 5.40% | 0.00% | 1.08% | 93.55% | NA |
| Indica III | 913 | 1.10% | 0.40% | 0.99% | 97.48% | NA |
| Indica Intermediate | 786 | 3.10% | 0.00% | 1.02% | 95.93% | NA |
| Temperate Japonica | 767 | 5.60% | 0.00% | 0.39% | 94.00% | NA |
| Tropical Japonica | 504 | 3.40% | 0.00% | 0.40% | 96.23% | NA |
| Japonica Intermediate | 241 | 3.30% | 0.40% | 1.24% | 95.02% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 72.92% | 26.04% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 6.67% | 91.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607439497 | C -> T | LOC_Os06g13500.1 | missense_variant ; p.Arg1241Lys; MODERATE | nonsynonymous_codon ; R1241K | Average:8.961; most accessible tissue: Minghui63 panicle, score: 25.313 | benign  |
-0.384 |
TOLERATED | 0.50 |
| vg0607439497 | C -> DEL | LOC_Os06g13500.1 | N | frameshift_variant | Average:8.961; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |