Search for Variation information by Variation ID:
Detailed information for vg0409515338:
| Variant ID: vg0409515338 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515338 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CACTTGCCGAACTTGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTCCGAAAAATCCTTAGGCACTACTTTCTTGTTATAAT[G/A]
CCTAGCAACTCGTTCCTTATCTCTGGTAACCTTAGCAAGGGCTCGTAAACGCGATTGAACCAAGTCCTCCCTCTCATCGGCCATAAGGTTATAATATTCA
Reverse complement sequence
TGAATATTATAACCTTATGGCCGATGAGAGGGAGGACTTGGTTCAATCGCGTTTACGAGCCCTTGCTAAGGTTACCAGAGATAAGGAACGAGTTGCTAGG[C/T]
ATTATAACAAGAAAGTAGTGCCTAAGGATTTTTCGGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACAAGTTCGGCAAGTG
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 | 89.20% | 0.60% | 1.38% | 8.80% | NA |
| All Indica | 2759 | 97.70% | 0.90% | 1.38% | 0.00% | NA |
| All Japonica | 1512 | 72.80% | 0.20% | 1.26% | 25.79% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 97.60% | 1.50% | 0.86% | 0.00% | NA |
| Indica III | 913 | 95.70% | 1.10% | 3.18% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 0.80% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 30.00% | 0.60% | 3.37% | 66.07% | NA |
| Japonica Intermediate | 241 | 80.10% | 0.00% | 0.83% | 19.09% | NA |
| VI/Aromatic | 96 | 69.80% | 0.00% | 4.17% | 26.04% | NA |
| Intermediate | 90 | 94.40% | 0.00% | 4.44% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515338 | G -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:23.632; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0409515338 | G -> A | LOC_Os04g17380.1 | missense_variant ; p.His90Tyr; MODERATE | nonsynonymous_codon ; H90Y | Average:23.632; most accessible tissue: Minghui63 panicle, score: 34.226 | benign  |
0.595 |
TOLERATED | 0.47 |