Search for Variation information by Variation ID:
Detailed information for vg0620603154:
| Variant ID: vg0620603154 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20603154 |
| Reference Allele: G | Alternative Allele: A,C |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACCCCAACCGGAGGCATACGTGTCCAAAATAGAGGAACCTCTAACGATCGAGCCGCTCACTGAACCATCCACTTCTGCTAGCTCGATTGATGAGAAGGTT[G/A,C]
CTAAGCAGCCGTCCGTCGAGAATGAAGAAATTCAGACTCCGGATCGTGCCGCAATTCTGTTCAGGGACGATTTTAACGAAGACTATGGCAATACCCTGAA
Reverse complement sequence
TTCAGGGTATTGCCATAGTCTTCGTTAAAATCGTCCCTGAACAGAATTGCGGCACGATCCGGAGTCTGAATTTCTTCATTCTCGACGGACGGCTGCTTAG[C/T,G]
AACCTTCTCATCAATCGAGCTAGCAGAAGTGGATGGTTCAGTGAGCGGCTCGATCGTTAGAGGTTCCTCTATTTTGGACACGTATGCCTCCGGTTGGGGT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.40% | 1.40% | 0.04% | 1.14% | NA |
| All Indica | 2759 | 99.60% | 0.30% | 0.07% | 0.07% | NA |
| All Japonica | 1512 | 96.50% | 0.20% | 0.00% | 3.31% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.30% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 99.40% | 0.40% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 82.60% | 1.20% | 0.00% | 16.18% | NA |
| VI/Aromatic | 96 | 47.90% | 52.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 7.80% | 0.00% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620603154 | G -> C | LOC_Os06g35340.1 | missense_variant ; p.Ala200Pro; MODERATE | N | Average:5.229; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |
| vg0620603154 | G -> A | LOC_Os06g35340.1 | missense_variant ; p.Ala200Thr; MODERATE | nonsynonymous_codon ; A200T | Average:5.229; most accessible tissue: Minghui63 flower, score: 9.27 | benign  |
0.343 |
TOLERATED | 0.26 |
| vg0620603154 | G -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:5.229; most accessible tissue: Minghui63 flower, score: 9.27 | N | N | N | N |