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Detailed information for vg0605310590:
| Variant ID: vg0605310590 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 5310590 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, T: 0.05, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
ATTTGGTGAATGATTAAAGGACTAACACTAAACATTTATGTTTTGCATCAAAGAACTTTGGAATCGACGGGCAACTGGTGGTTAACTATGCATCATCGAT[G/T]
GCATGGGGCTGAAAGGCTGTACCTGCTGGAGAGAGGAAACTTCAATCAACATGGAAAAACCTGTGTACAAAATTTACTTGCCGAAACACTCATCATGTAA
Reverse complement sequence
TTACATGATGAGTGTTTCGGCAAGTAAATTTTGTACACAGGTTTTTCCATGTTGATTGAAGTTTCCTCTCTCCAGCAGGTACAGCCTTTCAGCCCCATGC[C/A]
ATCGATGATGCATAGTTAACCACCAGTTGCCCGTCGATTCCAAAGTTCTTTGATGCAAAACATAAATGTTTAGTGTTAGTCCTTTAATCATTCACCAAAT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.90% | 2.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 88.50% | 11.20% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0605310590 | G -> T | LOC_Os06g10340.1 | missense_variant ; p.Met90Ile; MODERATE | nonsynonymous_codon ; M90I | Average:65.955; most accessible tissue: Minghui63 flower, score: 77.844 | benign  |
0.721 |
TOLERATED | 0.12 |