Search for Variation information by Variation ID:
Detailed information for vg1209388336:
| Variant ID: vg1209388336 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9388336 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 272. )
Flanking Sequence (100 bp) in Reference Genome:
TTCATCGACCCTCGGAAAGTAAACGTCGCAATGCTCGACCAATATCCGCAAGCCACAGAGGACAATCTCGTCCATCTCCTGAAGGCGCAGCATTACAAGA[T/C]
GTTCATACTGTTGCCGTACAACACAAAGTTAGTTTAATTTTACTGTCTTCCTATACCAAATTTCATTCCCGTACGAACTTGCTAAGTGTTTCATATGTAA
Reverse complement sequence
TTACATATGAAACACTTAGCAAGTTCGTACGGGAATGAAATTTGGTATAGGAAGACAGTAAAATTAAACTAACTTTGTGTTGTACGGCAACAGTATGAAC[A/G]
TCTTGTAATGCTGCGCCTTCAGGAGATGGACGAGATTGTCCTCTGTGGCTTGCGGATATTGGTCGAGCATTGCGACGTTTACTTTCCGAGGGTCGATGAA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.50% | 0.10% | 7.93% | 0.40% | NA |
| All Indica | 2759 | 87.70% | 0.20% | 11.56% | 0.51% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 79.20% | 0.40% | 18.59% | 1.86% | NA |
| Indica I | 595 | 99.20% | 0.00% | 0.67% | 0.17% | NA |
| Indica II | 465 | 70.10% | 1.10% | 28.60% | 0.22% | NA |
| Indica III | 913 | 90.10% | 0.00% | 9.31% | 0.55% | NA |
| Indica Intermediate | 786 | 86.60% | 0.10% | 12.34% | 0.89% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1209388336 | T -> C | LOC_Os12g16400.1 | missense_variant ; p.Met717Thr; MODERATE | nonsynonymous_codon ; M717T | Average:39.485; most accessible tissue: Minghui63 flag leaf, score: 64.867 | benign  |
-1.107 |
TOLERATED | 1.00 |
| vg1209388336 | T -> DEL | LOC_Os12g16400.1 | N | frameshift_variant | Average:39.485; most accessible tissue: Minghui63 flag leaf, score: 64.867 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209388336 | NA | 8.11E-09 | mr1024_2 | Ind_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 |
| vg1209388336 | 2.75E-06 | NA | mr1584_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 |
| vg1209388336 | 9.83E-09 | 9.84E-09 | mr1584_2 | 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 |
| vg1209388336 | NA | 8.01E-06 | mr1928_2 | Ind_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 |