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Detailed information for vg0614964955:
| Variant ID: vg0614964955 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14964955 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 213. )
Flanking Sequence (100 bp) in Reference Genome:
ATGGTGGCTAACAAACGAGGCAAATTATCATAAGAAGCTTCAAATGTGCCATACCTCATCTCAATGATCTTTTGTTTGGCTCTCCAGGCCTTTGCATAGG[T/A]
TATGGTGTACTTGAATTTGTTCTCGATGTGCCTAATAATTGATTTTGGTTCAAAGCCAATGTTACCAACAACACTGCTGTACATCTCACTTGCCACAAAA
Reverse complement sequence
TTTTGTGGCAAGTGAGATGTACAGCAGTGTTGTTGGTAACATTGGCTTTGAACCAAAATCAATTATTAGGCACATCGAGAACAAATTCAAGTACACCATA[A/T]
CCTATGCAAAGGCCTGGAGAGCCAAACAAAAGATCATTGAGATGAGGTATGGCACATTTGAAGCTTCTTATGATAATTTGCCTCGTTTGTTAGCCACCAT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.50% | 0.00% | 7.45% | 92.07% | NA |
| All Indica | 2759 | 0.70% | 0.00% | 0.43% | 98.88% | NA |
| All Japonica | 1512 | 0.10% | 0.10% | 22.16% | 77.65% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.37% | 99.26% | NA |
| Indica I | 595 | 0.80% | 0.00% | 0.84% | 98.32% | NA |
| Indica II | 465 | 0.60% | 0.00% | 0.00% | 99.35% | NA |
| Indica III | 913 | 0.10% | 0.00% | 0.11% | 99.78% | NA |
| Indica Intermediate | 786 | 1.30% | 0.00% | 0.76% | 97.96% | NA |
| Temperate Japonica | 767 | 0.10% | 0.10% | 23.99% | 75.75% | NA |
| Tropical Japonica | 504 | 0.20% | 0.00% | 14.88% | 84.92% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 31.54% | 68.46% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 4.44% | 95.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614964955 | T -> A | LOC_Os06g25580.1 | missense_variant ; p.Thr338Ser; MODERATE | nonsynonymous_codon ; T338S | Average:11.936; most accessible tissue: Minghui63 young leaf, score: 23.613 | benign  |
0.062 |
TOLERATED | 1.00 |
| vg0614964955 | T -> DEL | LOC_Os06g25580.1 | N | frameshift_variant | Average:11.936; most accessible tissue: Minghui63 young leaf, score: 23.613 | N | N | N | N |