Search for Variation information by Variation ID:
Detailed information for vg0411444492:
| Variant ID: vg0411444492 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 11444492 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACAATTCAAGCCTCGAAGTCCAGAAAAGAAGATTCCTATAGACCCCAGTGTCAGGAACTTCTTTAGGGGTATGTCTGCATCTGTCAAGAGGAGCATCTT[C/T]
TGGAAAGTCCAAACCAGTCCCTCAGCTTGGAGAGCAACCAAACCAGGAGATCGAGCCATTGGTGACCGGTAAAGAAATGACGATAGAACAATTTATTACT
Reverse complement sequence
AGTAATAAATTGTTCTATCGTCATTTCTTTACCGGTCACCAATGGCTCGATCTCCTGGTTTGGTTGCTCTCCAAGCTGAGGGACTGGTTTGGACTTTCCA[G/A]
AAGATGCTCCTCTTGACAGATGCAGACATACCCCTAAAGAAGTTCCTGACACTGGGGTCTATAGGAATCTTCTTTTCTGGACTTCGAGGCTTGAATTGTC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.00% | 1.40% | 3.77% | 45.85% | NA |
| All Indica | 2759 | 25.20% | 0.00% | 4.10% | 70.68% | NA |
| All Japonica | 1512 | 94.80% | 4.10% | 0.20% | 0.93% | NA |
| Aus | 269 | 17.10% | 0.00% | 21.93% | 60.97% | NA |
| Indica I | 595 | 9.70% | 0.00% | 1.34% | 88.91% | NA |
| Indica II | 465 | 38.90% | 0.00% | 3.01% | 58.06% | NA |
| Indica III | 913 | 27.10% | 0.00% | 6.46% | 66.48% | NA |
| Indica Intermediate | 786 | 26.70% | 0.00% | 4.07% | 69.21% | NA |
| Temperate Japonica | 767 | 92.40% | 6.60% | 0.39% | 0.52% | NA |
| Tropical Japonica | 504 | 97.40% | 1.60% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 96.70% | 1.20% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 64.40% | 2.20% | 3.33% | 30.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0411444492 | C -> DEL | LOC_Os04g20460.1 | N | frameshift_variant | Average:6.907; most accessible tissue: Callus, score: 17.301 | N | N | N | N |
| vg0411444492 | C -> T | LOC_Os04g20460.1 | missense_variant ; p.Ser119Phe; MODERATE | nonsynonymous_codon ; S119F | Average:6.907; most accessible tissue: Callus, score: 17.301 | possibly damaging  |
1.806 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0411444492 | 2.09E-06 | 4.19E-08 | mr1035 | Jap_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 |
| vg0411444492 | NA | 6.25E-07 | mr1626 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0411444492 | NA | 3.49E-08 | mr1631_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |