Search for Variation information by Variation ID:
Detailed information for vg1120931997:
| Variant ID: vg1120931997 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20931997 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTGACGTTACGAACCATTGGGTCTAGTACCAGGGGGTACCGCCCCGGGTGGACCACTCGGTCAGGATGATCCGAGCGGTCAAACTTGATTGTTGTCTCT[G/A]
ACCACCAAAGATATTGGGGCATATCGGGCTGGACAGCATTGATCTCCCGTTCAGTCAGCTTTTGCTTTCTCTTGGATATTCATAAGCCAGGGGTCCGCCA
Reverse complement sequence
TGGCGGACCCCTGGCTTATGAATATCCAAGAGAAAGCAAAAGCTGACTGAACGGGAGATCAATGCTGTCCAGCCCGATATGCCCCAATATCTTTGGTGGT[C/T]
AGAGACAACAATCAAGTTTGACCGCTCGGATCATCCTGACCGAGTGGTCCACCCGGGGCGGTACCCCCTGGTACTAGACCCAATGGTTCGTAACGTCAAG
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 | 93.50% | 5.70% | 0.80% | 0.00% | NA |
| All Indica | 2759 | 95.10% | 4.30% | 0.58% | 0.00% | NA |
| All Japonica | 1512 | 98.50% | 0.10% | 1.32% | 0.00% | NA |
| Aus | 269 | 46.80% | 52.80% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 84.90% | 13.30% | 1.72% | 0.00% | NA |
| Indica III | 913 | 98.40% | 1.10% | 0.55% | 0.00% | NA |
| Indica Intermediate | 786 | 93.80% | 5.90% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 96.40% | 0.00% | 3.57% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1120931997 | G -> A | LOC_Os11g35700.1 | missense_variant ; p.Ser643Leu; MODERATE | nonsynonymous_codon ; S643L | Average:36.672; most accessible tissue: Minghui63 young leaf, score: 64.378 | benign  |
0.622 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1120931997 | 6.53E-08 | 2.39E-09 | mr1309 | 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 |