Search for Variation information by Variation ID:
Detailed information for vg0334134764:
| Variant ID: vg0334134764 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34134764 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 372. )
Flanking Sequence (100 bp) in Reference Genome:
GTGAAAGAGATCCGTATTCTCGGGCCTATGTACCTACACAACATGTTTCCTTTCGAGAGGTACATGGGCGTTCTGAAGAAGTATGTTCGTAACCGTGCTC[G/A]
TCCAGAGGCAAGCATCGCCAAGGGTTATGGAACAGAGGAGGTCATCGAATTTTGCGTAGAATTTATCGAAGACCTTCGCCCAATCGGGGTACCTGAATCA
Reverse complement sequence
TGATTCAGGTACCCCGATTGGGCGAAGGTCTTCGATAAATTCTACGCAAAATTCGATGACCTCCTCTGTTCCATAACCCTTGGCGATGCTTGCCTCTGGA[C/T]
GAGCACGGTTACGAACATACTTCTTCAGAACGCCCATGTACCTCTCGAAAGGAAACATGTTGTGTAGGTACATAGGCCCGAGAATACGGATCTCTTTCAC
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 | 2.20% | 0.40% | 7.62% | 89.76% | NA |
| All Indica | 2759 | 2.20% | 0.70% | 9.35% | 87.75% | NA |
| All Japonica | 1512 | 1.30% | 0.10% | 1.52% | 97.16% | NA |
| Aus | 269 | 7.10% | 0.00% | 26.02% | 66.91% | NA |
| Indica I | 595 | 1.50% | 0.00% | 4.03% | 94.45% | NA |
| Indica II | 465 | 1.70% | 0.20% | 4.30% | 93.76% | NA |
| Indica III | 913 | 2.80% | 1.50% | 17.63% | 77.98% | NA |
| Indica Intermediate | 786 | 2.40% | 0.40% | 6.74% | 90.46% | NA |
| Temperate Japonica | 767 | 0.30% | 0.00% | 0.52% | 99.22% | NA |
| Tropical Japonica | 504 | 2.80% | 0.00% | 3.57% | 93.65% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.40% | 0.41% | 97.93% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 6.25% | 92.71% | NA |
| Intermediate | 90 | 4.40% | 0.00% | 3.33% | 92.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334134764 | G -> A | LOC_Os03g60010.1 | missense_variant ; p.Arg778His; MODERATE | nonsynonymous_codon ; R778H | Average:5.152; most accessible tissue: Zhenshan97 root, score: 12.891 | benign  |
0.521 |
DELETERIOUS | 0.02 |
| vg0334134764 | G -> DEL | LOC_Os03g60010.1 | N | frameshift_variant | Average:5.152; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |