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Detailed information for vg0424400640:
| Variant ID: vg0424400640 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24400640 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.04, others allele: 0.00, population size: 318. )
Flanking Sequence (100 bp) in Reference Genome:
GATAACATAGCATCTAGTAATTCATGAGCATGGTCCACTTTGTGAGCTTTGCATAAACCATCTACTAGTGCACCATATGTCACAACATTTGGAGCAAGTG[T/C]
GTGTCTGTCCTCACATGGAAAGTAAAAATCAGAATCGGCGCTATCAGAAGTTCCAATTAATTTGGCATAGACTTCAAAAGCCTTACTGATGTTGCCTGCT
Reverse complement sequence
AGCAGGCAACATCAGTAAGGCTTTTGAAGTCTATGCCAAATTAATTGGAACTTCTGATAGCGCCGATTCTGATTTTTACTTTCCATGTGAGGACAGACAC[A/G]
CACTTGCTCCAAATGTTGTGACATATGGTGCACTAGTAGATGGTTTATGCAAAGCTCACAAAGTGGACCATGCTCATGAATTACTAGATGCTATGTTATC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 61.70% | 38.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 87.80% | 12.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.90% | 6.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424400640 | T -> C | LOC_Os04g41140.1 | missense_variant ; p.Thr608Ala; MODERATE | nonsynonymous_codon ; T608A | Average:49.523; most accessible tissue: Zhenshan97 young leaf, score: 80.848 | benign  |
0.137 |
TOLERATED | 0.98 |