Search for Variation information by Variation ID:
Detailed information for vg0905621407:
| Variant ID: vg0905621407 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5621407 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, C: 0.06, others allele: 0.00, population size: 218. )
Flanking Sequence (100 bp) in Reference Genome:
TGCCTCCTGACAAGCATGAATATAATCTCTTCCTCCAGCTTCAAACATCATTGATGGAAGGTCTTCACGATCACTAGTCAACGTCATGCGAACACGACTA[T/C]
TCTCCTCATTGGGGTCATGGGGAATTTGGCGATACTCGGGGACAATGTTGTAGCCTACTTCAAATGCCATCATTCTCAGCTCCCTGACGAATCCTACTGC
Reverse complement sequence
GCAGTAGGATTCGTCAGGGAGCTGAGAATGATGGCATTTGAAGTAGGCTACAACATTGTCCCCGAGTATCGCCAAATTCCCCATGACCCCAATGAGGAGA[A/G]
TAGTCGTGTTCGCATGACGTTGACTAGTGATCGTGAAGACCTTCCATCAATGATGTTTGAAGCTGGAGGAAGAGATTATATTCATGCTTGTCAGGAGGCA
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 | 92.40% | 7.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 82.30% | 17.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 82.90% | 17.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.10% | 6.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 90.70% | 9.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 82.70% | 17.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 54.80% | 45.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0905621407 | T -> C | LOC_Os09g10310.1 | missense_variant ; p.Asn41Ser; MODERATE | nonsynonymous_codon | Average:41.722; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 | benign  |
0.829 |
DELETERIOUS | 0.00 |