Search for Variation information by Variation ID:
Detailed information for vg1011512457:
| Variant ID: vg1011512457 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 11512457 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTGAAGCCGAGTAGTGCGCCCTTTCACGGAGTCATCCCCGGGCTGTCTTCTACTCCACTCGGCCAGATCACCTTGCCGGTCACCTTCGGCACTTGGGAGA[G/A]
CTTTTGTACAGAAAATATCTGCTTTGAAGTTGCTGATTTCGAGACAGCGTATCACGCTATACTTGGACGCCCGGCGTTAGCCAAATTCATGGCAGTCCCA
Reverse complement sequence
TGGGACTGCCATGAATTTGGCTAACGCCGGGCGTCCAAGTATAGCGTGATACGCTGTCTCGAAATCAGCAACTTCAAAGCAGATATTTTCTGTACAAAAG[C/T]
TCTCCCAAGTGCCGAAGGTGACCGGCAAGGTGATCTGGCCGAGTGGAGTAGAAGACAGCCCGGGGATGACTCCGTGAAAGGGCGCACTACTCGGCTTCAG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.80% | 19.10% | 26.24% | 13.84% | NA |
| All Indica | 2759 | 36.00% | 19.90% | 34.94% | 9.17% | NA |
| All Japonica | 1512 | 54.80% | 13.70% | 5.75% | 25.79% | NA |
| Aus | 269 | 16.00% | 22.70% | 59.85% | 1.49% | NA |
| Indica I | 595 | 50.90% | 14.10% | 28.24% | 6.72% | NA |
| Indica II | 465 | 31.00% | 20.20% | 32.04% | 16.77% | NA |
| Indica III | 913 | 31.00% | 23.40% | 39.10% | 6.46% | NA |
| Indica Intermediate | 786 | 33.60% | 19.80% | 36.90% | 9.67% | NA |
| Temperate Japonica | 767 | 88.00% | 2.10% | 1.96% | 7.95% | NA |
| Tropical Japonica | 504 | 14.30% | 32.50% | 10.71% | 42.46% | NA |
| Japonica Intermediate | 241 | 33.60% | 11.20% | 7.47% | 47.72% | NA |
| VI/Aromatic | 96 | 19.80% | 69.80% | 9.38% | 1.04% | NA |
| Intermediate | 90 | 51.10% | 21.10% | 21.11% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1011512457 | G -> A | LOC_Os10g22240.1 | missense_variant ; p.Ser651Asn; MODERATE | nonsynonymous_codon ; S651N | Average:17.305; most accessible tissue: Minghui63 panicle, score: 34.226 | benign  |
-0.7 |
TOLERATED | 1.00 |
| vg1011512457 | G -> DEL | LOC_Os10g22240.1 | N | frameshift_variant | Average:17.305; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1011512457 | NA | 2.01E-06 | mr1398 | 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 |
| vg1011512457 | 4.12E-06 | 1.53E-10 | mr1551 | 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 |
| vg1011512457 | NA | 3.96E-06 | mr1606 | 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 |
| vg1011512457 | NA | 8.48E-07 | mr1206_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 |