Search for Variation information by Variation ID:
Detailed information for vg1211633613:
| Variant ID: vg1211633613 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 11633613 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
TACCCCCAACTGATTTCTCCCCACGAATGGCACAGATATAAACGAGTGGGAAGCTCCAGAGTCGAACAAAATGGTAGCAGGGATGGAATGTATGAGGAAC[G/A]
TACCAACGATGACGTCTGGAGTTGTCAGCACGCCCTCGGCCGTCACGTGGTTCACACGGCCCCGAATGACATCCTTACCACCATTGTTGGAGCGGGGAGG
Reverse complement sequence
CCTCCCCGCTCCAACAATGGTGGTAAGGATGTCATTCGGGGCCGTGTGAACCACGTGACGGCCGAGGGCGTGCTGACAACTCCAGACGTCATCGTTGGTA[C/T]
GTTCCTCATACATTCCATCCCTGCTACCATTTTGTTCGACTCTGGAGCTTCCCACTCGTTTATATCTGTGCCATTCGTGGGGAGAAATCAGTTGGGGGTA
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 | 85.90% | 4.60% | 3.39% | 6.12% | NA |
| All Indica | 2759 | 95.00% | 2.30% | 1.63% | 1.05% | NA |
| All Japonica | 1512 | 80.20% | 0.30% | 2.58% | 17.00% | NA |
| Aus | 269 | 30.90% | 43.90% | 25.28% | 0.00% | NA |
| Indica I | 595 | 95.60% | 1.00% | 0.17% | 3.19% | NA |
| Indica II | 465 | 96.10% | 1.10% | 2.37% | 0.43% | NA |
| Indica III | 913 | 95.60% | 2.60% | 1.75% | 0.00% | NA |
| Indica Intermediate | 786 | 93.30% | 3.60% | 2.16% | 1.02% | NA |
| Temperate Japonica | 767 | 95.30% | 0.00% | 1.17% | 3.52% | NA |
| Tropical Japonica | 504 | 67.70% | 0.40% | 3.77% | 28.17% | NA |
| Japonica Intermediate | 241 | 58.10% | 0.80% | 4.56% | 36.51% | NA |
| VI/Aromatic | 96 | 67.70% | 27.10% | 4.17% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 8.90% | 4.44% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1211633613 | G -> DEL | LOC_Os12g19980.1 | N | frameshift_variant | Average:32.82; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | N | N | N | N |
| vg1211633613 | G -> A | LOC_Os12g19980.1 | missense_variant ; p.Thr716Met; MODERATE | nonsynonymous_codon ; T716M | Average:32.82; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | benign  |
0.762 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1211633613 | 1.87E-06 | 2.96E-10 | mr1016 | 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 |
| vg1211633613 | 2.01E-07 | 4.85E-11 | mr1019 | 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 |
| vg1211633613 | 1.46E-06 | NA | mr1055 | 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 |
| vg1211633613 | 1.89E-08 | NA | mr1055_2 | 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 |
| vg1211633613 | 1.13E-06 | NA | mr1132_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 |
| vg1211633613 | 7.66E-08 | NA | mr1390_2 | 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 |
| vg1211633613 | 9.02E-09 | NA | mr1490_2 | 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 |