Search for Variation information by Variation ID:
Detailed information for vg1120088079:
| Variant ID: vg1120088079 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20088079 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
TGTTTATCTGGAAAAGTTTGGGATGGAGATTTTTTAAAAGTATCCGATTCTGATATACAGCCAATTGAAGATGGAGAACCCAAGCTATTATTTTGAGGGC[G/A]
TCGTGGAGGGTTCGAACGTCTACACCATGGATAGAGTAGATGATCTCGATGACAAACAAGGTCAAGGTTTTATGTCGGCCGATGATTTGGAGGAAATTGA
Reverse complement sequence
TCAATTTCCTCCAAATCATCGGCCGACATAAAACCTTGACCTTGTTTGTCATCGAGATCATCTACTCTATCCATGGTGTAGACGTTCGAACCCTCCACGA[C/T]
GCCCTCAAAATAATAGCTTGGGTTCTCCATCTTCAATTGGCTGTATATCAGAATCGGATACTTTTAAAAAATCTCCATCCCAAACTTTTCCAGATAAACA
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 | 92.90% | 3.50% | 2.75% | 0.83% | NA |
| All Indica | 2759 | 99.70% | 0.10% | 0.14% | 0.04% | NA |
| All Japonica | 1512 | 78.50% | 10.80% | 8.27% | 2.45% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.30% | 0.25% | 0.13% | NA |
| Temperate Japonica | 767 | 79.70% | 16.70% | 2.74% | 0.91% | NA |
| Tropical Japonica | 504 | 69.80% | 5.60% | 19.64% | 4.96% | NA |
| Japonica Intermediate | 241 | 92.90% | 2.90% | 2.07% | 2.07% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1120088079 | G -> A | LOC_Os11g34290.1 | missense_variant ; p.Val985Ile; MODERATE | nonsynonymous_codon ; V985I | Average:50.048; most accessible tissue: Minghui63 flag leaf, score: 78.154 | benign  |
0.494 |
TOLERATED | 0.13 |
| vg1120088079 | G -> DEL | LOC_Os11g34290.1 | N | frameshift_variant | Average:50.048; most accessible tissue: Minghui63 flag leaf, score: 78.154 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1120088079 | 1.32E-06 | NA | mr1410 | 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 |
| vg1120088079 | 2.20E-06 | NA | mr1124_2 | 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 |
| vg1120088079 | 7.56E-06 | 4.11E-06 | mr1124_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 |
| vg1120088079 | 3.83E-06 | NA | mr1410_2 | 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 |