Search for Variation information by Variation ID:
Detailed information for vg0906481295:
| Variant ID: vg0906481295 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 6481295 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCGGCTTGAACGGTATATCCAAGGACATCAGTCCTAAGGCCCATTTTGCGATTCGCCCGTTTGCTTCGCGATTATGGAGGATATCGCCGAGTGGAAACGA[T/C]
GTAACCACCGTGACCGAGTGGCCTTGGAAGTAGTGGGATAATTTCCTGACGGTGATTAGAACACCGTACAACAGCTTCTGAACTTGAGGATATCTCGTCT
Reverse complement sequence
AGACGAGATATCCTCAAGTTCAGAAGCTGTTGTACGGTGTTCTAATCACCGTCAGGAAATTATCCCACTACTTCCAAGGCCACTCGGTCACGGTGGTTAC[A/G]
TCGTTTCCACTCGGCGATATCCTCCATAATCGCGAAGCAAACGGGCGAATCGCAAAATGGGCCTTAGGACTGATGTCCTTGGATATACCGTTCAAGCCGC
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 | 83.00% | 9.80% | 7.19% | 0.02% | NA |
| All Indica | 2759 | 72.50% | 15.90% | 11.60% | 0.04% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 96.70% | 1.90% | 1.49% | 0.00% | NA |
| Indica I | 595 | 86.90% | 7.90% | 5.21% | 0.00% | NA |
| Indica II | 465 | 72.00% | 18.90% | 9.03% | 0.00% | NA |
| Indica III | 913 | 60.00% | 20.30% | 19.61% | 0.11% | NA |
| Indica Intermediate | 786 | 76.30% | 15.00% | 8.65% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 76.00% | 8.30% | 15.62% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0906481295 | T -> DEL | LOC_Os09g11610.1 | N | frameshift_variant | Average:36.477; most accessible tissue: Minghui63 flag leaf, score: 66.004 | N | N | N | N |
| vg0906481295 | T -> C | LOC_Os09g11610.1 | synonymous_variant ; p.Thr804Thr; LOW | synonymous_codon | Average:36.477; most accessible tissue: Minghui63 flag leaf, score: 66.004 | N | N | N | N |
| vg0906481295 | T -> C | LOC_Os09g11610.1 | synonymous_variant ; p.Thr804Thr; LOW | nonsynonymous_codon ; T804M | Average:36.477; most accessible tissue: Minghui63 flag leaf, score: 66.004 | benign  |
1.27 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0906481295 | 5.39E-06 | 5.39E-06 | mr1025 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |