Search for Variation information by Variation ID:
Detailed information for vg0614962467:
| Variant ID: vg0614962467 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14962467 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCGCAAATAAGCACGTATGATAATAACAACTTATTTACTTACAGTGAACTGGAGCAACCAAGCCTTGCTAGGCCCGACTGTAGAGTACGGAGGAAGGGTG[G/T]
TGGTCGGTCCTAGGTGTGGAAGGCGCATCACCTGCTCGAAGCGCGCAGTGATATCCTCCTTCCACCCAAAAACACCGTCGACGGGACCAACTGGTGCTCC
Reverse complement sequence
GGAGCACCAGTTGGTCCCGTCGACGGTGTTTTTGGGTGGAAGGAGGATATCACTGCGCGCTTCGAGCAGGTGATGCGCCTTCCACACCTAGGACCGACCA[C/A]
CACCCTTCCTCCGTACTCTACAGTCGGGCCTAGCAAGGCTTGGTTGCTCCAGTTCACTGTAAGTAAATAAGTTGTTATTATCATACGTGCTTATTTGCGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.70% | 0.10% | 3.45% | 60.79% | NA |
| All Indica | 2759 | 4.50% | 0.10% | 4.17% | 91.23% | NA |
| All Japonica | 1512 | 82.30% | 0.20% | 1.59% | 15.94% | NA |
| Aus | 269 | 74.70% | 0.00% | 2.23% | 23.05% | NA |
| Indica I | 595 | 5.20% | 0.00% | 1.68% | 93.11% | NA |
| Indica II | 465 | 2.20% | 0.00% | 1.29% | 96.56% | NA |
| Indica III | 913 | 1.90% | 0.00% | 7.78% | 90.36% | NA |
| Indica Intermediate | 786 | 8.50% | 0.30% | 3.56% | 87.66% | NA |
| Temperate Japonica | 767 | 96.00% | 0.30% | 0.26% | 3.52% | NA |
| Tropical Japonica | 504 | 58.90% | 0.20% | 3.57% | 37.30% | NA |
| Japonica Intermediate | 241 | 87.60% | 0.00% | 1.66% | 10.79% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 14.58% | 9.38% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 4.44% | 48.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614962467 | G -> T | LOC_Os06g25580.1 | missense_variant ; p.Thr991Asn; MODERATE | nonsynonymous_codon ; T991N | Average:4.786; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.065 |
TOLERATED | 0.70 |
| vg0614962467 | G -> DEL | LOC_Os06g25580.1 | N | frameshift_variant | Average:4.786; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |