Search for Variation information by Variation ID:
Detailed information for vg0719562414:
| Variant ID: vg0719562414 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562414 |
| 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: 295. )
Flanking Sequence (100 bp) in Reference Genome:
CCTACGAGCGCTGCTGTTCGTAACCATCAACGATTGGCCTGTACTTAGCAACCTATCCGGACAGTCCAACAAGGGGTACAAGGCTTGCACTCACTGTATG[G/A]
ATGAAACAGAAAGTACGTATCTTAAGCACTGTAGGAAGGTTGTATACATGGGTCATCGTCGATTCCTTGCAGCAAACCACCCGGTACGGAAGAAAGGCAA
Reverse complement sequence
TTGCCTTTCTTCCGTACCGGGTGGTTTGCTGCAAGGAATCGACGATGACCCATGTATACAACCTTCCTACAGTGCTTAAGATACGTACTTTCTGTTTCAT[C/T]
CATACAGTGAGTGCAAGCCTTGTACCCCTTGTTGGACTGTCCGGATAGGTTGCTAAGTACAGGCCAATCGTTGATGGTTACGAACAGCAGCGCTCGTAGG
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 | 0.60% | 0.10% | 34.51% | 64.81% | NA |
| All Indica | 2759 | 0.10% | 0.20% | 23.49% | 76.22% | NA |
| All Japonica | 1512 | 1.50% | 0.00% | 47.82% | 50.66% | NA |
| Aus | 269 | 0.40% | 0.00% | 71.38% | 28.25% | NA |
| Indica I | 595 | 0.00% | 0.20% | 5.38% | 94.45% | NA |
| Indica II | 465 | 0.20% | 0.00% | 20.22% | 79.57% | NA |
| Indica III | 913 | 0.10% | 0.10% | 41.29% | 58.49% | NA |
| Indica Intermediate | 786 | 0.10% | 0.40% | 18.45% | 81.04% | NA |
| Temperate Japonica | 767 | 0.30% | 0.00% | 23.86% | 75.88% | NA |
| Tropical Japonica | 504 | 3.80% | 0.00% | 80.75% | 15.48% | NA |
| Japonica Intermediate | 241 | 0.80% | 0.00% | 55.19% | 43.98% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 41.67% | 58.33% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 31.11% | 68.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562414 | G -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:6.027; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0719562414 | G -> A | LOC_Os07g32740.1 | missense_variant ; p.Asp411Asn; MODERATE | nonsynonymous_codon ; D411N | Average:6.027; most accessible tissue: Zhenshan97 root, score: 12.891 | probably damaging  |
2.021 |
DELETERIOUS | 0.00 |