Search for Variation information by Variation ID:
Detailed information for vg1121623328:
| Variant ID: vg1121623328 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21623328 |
| Reference Allele: G | Alternative Allele: A,C |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTGGAAATTGGCGACGAACTGTTGCCACAGGTCTGCCCACGAAGAGATTGAGTAGGGAGGAAGATGCATCAGCCATGAACGTGCAGAACCTTTCAACGCA[G/A,C]
TTGGTAAATAATTTGCCAACGCGTTGTCGTCTGCTCCGGCAGTGTAGAGTACTGTGGAGTAGACTTGAAGGAACTCCTCTGGGTCGGTGCTCCCATCATA
Reverse complement sequence
TATGATGGGAGCACCGACCCAGAGGAGTTCCTTCAAGTCTACTCCACAGTACTCTACACTGCCGGAGCAGACGACAACGCGTTGGCAAATTATTTACCAA[C/T,G]
TGCGTTGAAAGGTTCTGCACGTTCATGGCTGATGCATCTTCCTCCCTACTCAATCTCTTCGTGGGCAGACCTGTGGCAACAGTTCGTCGCCAATTTCCAA
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 | 88.10% | 5.40% | 4.95% | 1.48% | C: 0.04% |
| All Indica | 2759 | 82.70% | 9.00% | 8.23% | 0.04% | C: 0.07% |
| All Japonica | 1512 | 95.00% | 0.30% | 0.46% | 4.30% | NA |
| Aus | 269 | 98.50% | 0.40% | 0.00% | 1.12% | NA |
| Indica I | 595 | 78.80% | 11.40% | 9.58% | 0.17% | NA |
| Indica II | 465 | 75.10% | 14.40% | 10.54% | 0.00% | NA |
| Indica III | 913 | 90.00% | 4.70% | 5.04% | 0.00% | C: 0.22% |
| Indica Intermediate | 786 | 81.60% | 8.90% | 9.54% | 0.00% | NA |
| Temperate Japonica | 767 | 93.20% | 0.40% | 0.65% | 5.74% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.40% | 0.41% | 6.64% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121623328 | G -> A | LOC_Os11g36640.1 | missense_variant ; p.Thr476Ile; MODERATE | nonsynonymous_codon ; T476I | Average:9.191; most accessible tissue: Minghui63 flag leaf, score: 15.952 | benign  |
1.271 |
DELETERIOUS | 0.00 |
| vg1121623328 | G -> DEL | LOC_Os11g36640.1 | N | frameshift_variant | Average:9.191; most accessible tissue: Minghui63 flag leaf, score: 15.952 | N | N | N | N |
| vg1121623328 | G -> C | LOC_Os11g36640.1 | missense_variant ; p.Thr476Ser; MODERATE | nonsynonymous_codon ; T476S | Average:9.191; most accessible tissue: Minghui63 flag leaf, score: 15.952 | benign |
0.289 |
TOLERATED | 0.11 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121623328 | 2.50E-06 | NA | mr1412 | 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 |
| vg1121623328 | 3.05E-06 | 3.06E-06 | mr1412 | 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 |