Search for Variation information by Variation ID:
Detailed information for vg1007671399:
| Variant ID: vg1007671399 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7671399 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 440. )
Flanking Sequence (100 bp) in Reference Genome:
ACCTTCAATGATGCTCCCCTCGGGTTTAGCTCTGTTACGAACGTACAACTTCAGAACTCCCATGTACCTTTCAAACGGCCACATTTCCCTTAGAAAAGCC[G/A]
GGCCACATAGTTTTGTTTGCTTCACCAGATGAACAGGGAGATGAACCATTATATCAAAGAAAGACAGTGGGAAAAACATCTCCAGGTGACAGAGGGTATT
Reverse complement sequence
AATACCCTCTGTCACCTGGAGATGTTTTTCCCACTGTCTTTCTTTGATATAATGGTTCATCTCCCTGTTCATCTGGTGAAGCAAACAAAACTATGTGGCC[C/T]
GGCTTTTCTAAGGGAAATGTGGCCGTTTGAAAGGTACATGGGAGTTCTGAAGTTGTACGTTCGTAACAGAGCTAAACCCGAGGGGAGCATCATTGAAGGT
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 | 16.00% | 0.30% | 14.47% | 69.26% | NA |
| All Indica | 2759 | 1.50% | 0.50% | 8.59% | 89.42% | NA |
| All Japonica | 1512 | 45.00% | 0.00% | 12.04% | 42.92% | NA |
| Aus | 269 | 0.70% | 0.40% | 75.09% | 23.79% | NA |
| Indica I | 595 | 0.30% | 0.50% | 1.34% | 97.82% | NA |
| Indica II | 465 | 1.70% | 0.60% | 15.91% | 81.72% | NA |
| Indica III | 913 | 1.30% | 0.50% | 7.89% | 90.25% | NA |
| Indica Intermediate | 786 | 2.50% | 0.30% | 10.56% | 86.64% | NA |
| Temperate Japonica | 767 | 62.80% | 0.00% | 12.52% | 24.64% | NA |
| Tropical Japonica | 504 | 11.30% | 0.00% | 11.31% | 77.38% | NA |
| Japonica Intermediate | 241 | 58.90% | 0.00% | 12.03% | 29.05% | NA |
| VI/Aromatic | 96 | 9.40% | 1.00% | 50.00% | 39.58% | NA |
| Intermediate | 90 | 22.20% | 0.00% | 16.67% | 61.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007671399 | G -> A | LOC_Os10g14130.1 | missense_variant ; p.Pro281Leu; MODERATE | nonsynonymous_codon ; P281L | Average:6.735; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 | benign  |
0.984 |
DELETERIOUS | 0.02 |
| vg1007671399 | G -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.735; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 | N | N | N | N |