Search for Variation information by Variation ID:
Detailed information for vg0121065564:
| Variant ID: vg0121065564 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 21065564 |
| Reference Allele: GGAA | Alternative Allele: AGAA,G |
| Primary Allele: GGAA | Secondary Allele: AGAA |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACTCATAGTGGGAAAACCCTGAAGAAATTGGCATCAAAGAAAGATTCATTGCTGAAGAAAGTAGAAAAGACAGAATGTTGTACTACTATGGTGCTCTGGG[GGAA/AGAA,G]
GAAGGAGGAAAATCTAGTCATAGAACAAGAGTCTCAGGAGATGGTGACACCGGTCGAGATGCAATCTCAAGATGAGGGAGGTGAAATGACAAATGAGAAG
Reverse complement sequence
CTTCTCATTTGTCATTTCACCTCCCTCATCTTGAGATTGCATCTCGACCGGTGTCACCATCTCCTGAGACTCTTGTTCTATGACTAGATTTTCCTCCTTC[TTCC/TTCT,C]
CCCAGAGCACCATAGTAGTACAACATTCTGTCTTTTCTACTTTCTTCAGCAATGAATCTTTCTTTGATGCCAATTTCTTCAGGGTTTTCCCACTATGAGT
Allele Frequencies:
| Populations | Population Size | Frequency of GGAA(primary allele) | Frequency of AGAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.40% | 1.30% | 0.06% | 2.16% | G: 0.04% |
| All Indica | 2759 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 93.20% | 0.00% | 0.20% | 6.61% | NA |
| Aus | 269 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 95.20% | 0.00% | 0.00% | 4.76% | NA |
| Japonica Intermediate | 241 | 68.50% | 0.00% | 1.24% | 30.29% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 0.00% | 2.22% | G: 2.22% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0121065564 | GGAA -> G | LOC_Os01g37660.1 | inframe_deletion ; p.Lys37del; MODERATE | inframe_variant | Average:50.328; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |
| vg0121065564 | GGAA -> AGAA | LOC_Os01g37660.1 | missense_variant ; p.Gly35Glu; MODERATE | nonsynonymous_codon ; G35E | Average:50.328; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | probably damaging  |
+2.107 |
N | N |
| vg0121065564 | GGAA -> DEL | LOC_Os01g37660.1 | N | frameshift_variant | Average:50.328; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |