Search for Variation information by Variation ID:
Detailed information for vg0329363247:
| Variant ID: vg0329363247 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29363247 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AACACCGGCCCCCGCGGCTGGAAGTAGCAACCACCAACCACCGACGGCGGCGACACCGACTGTACGGTGAAGAACCACCGGAACAGCCGAAGGGATGGGC[G/C]
CACCCCGATGAACATCTCGCACAGGTGCGCGAAGATGGCCAATGTCATTACCGCGTTGGGGGTGAGGTGCGCCATCTGGAGATCGTAAAACTCCAGAACA
Reverse complement sequence
TGTTCTGGAGTTTTACGATCTCCAGATGGCGCACCTCACCCCCAACGCGGTAATGACATTGGCCATCTTCGCGCACCTGTGCGAGATGTTCATCGGGGTG[C/G]
GCCCATCCCTTCGGCTGTTCCGGTGGTTCTTCACCGTACAGTCGGTGTCGCCGCCGTCGGTGGTTGGTGGTTGCTACTTCCAGCCGCGGGGGCCGGTGTT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.90% | 0.40% | 0.32% | 43.38% | NA |
| All Indica | 2759 | 37.30% | 0.00% | 0.51% | 62.20% | NA |
| All Japonica | 1512 | 99.40% | 0.10% | 0.07% | 0.46% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 52.60% | 0.00% | 0.17% | 47.23% | NA |
| Indica II | 465 | 37.80% | 0.00% | 0.65% | 61.51% | NA |
| Indica III | 913 | 27.60% | 0.00% | 0.55% | 71.85% | NA |
| Indica Intermediate | 786 | 36.60% | 0.00% | 0.64% | 62.72% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 52.10% | 18.80% | 0.00% | 29.17% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 0.00% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329363247 | G -> C | LOC_Os03g51320.1 | missense_variant ; p.Arg111Gly; MODERATE | nonsynonymous_codon ; R111G | Average:24.884; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | possibly damaging  |
1.657 |
DELETERIOUS | 0.00 |
| vg0329363247 | G -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:24.884; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | N | N | N | N |