Search for Variation information by Variation ID:
Detailed information for vg0100128986:
| Variant ID: vg0100128986 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 128986 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.62, T: 0.38, others allele: 0.00, population size: 200. )
Flanking Sequence (100 bp) in Reference Genome:
GTCAAGATGAATCATGCCCCTGCTCCTTGGCTGTTGAGTGCGCCGTCGAACACCATTGTCCACGTTTCGTTGTCAATTTGGTTGCCTGACCTGTTATCAG[T/G]
CATAGTCCAATCGGCTACGAAGTCGGCAAGTACCTGGGACTTGATGGTTGTTCGTGGCACAAAGCGGACATTAAATTGGCTTAGCTCGACTACCCATTTC
Reverse complement sequence
GAAATGGGTAGTCGAGCTAAGCCAATTTAATGTCCGCTTTGTGCCACGAACAACCATCAAGTCCCAGGTACTTGCCGACTTCGTAGCCGATTGGACTATG[A/C]
CTGATAACAGGTCAGGCAACCAAATTGACAACGAAACGTGGACAATGGTGTTCGACGGCGCACTCAACAGCCAAGGAGCAGGGGCATGATTCATCTTGAC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.80% | 17.40% | 3.79% | 3.07% | NA |
| All Indica | 2759 | 69.50% | 25.90% | 4.35% | 0.29% | NA |
| All Japonica | 1512 | 97.60% | 2.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 11.50% | 26.00% | 17.47% | 44.98% | NA |
| Indica I | 595 | 29.90% | 58.80% | 11.26% | 0.00% | NA |
| Indica II | 465 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 86.10% | 12.50% | 0.99% | 0.44% | NA |
| Indica Intermediate | 786 | 64.10% | 29.80% | 5.60% | 0.51% | NA |
| Temperate Japonica | 767 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 4.17% | 12.50% | NA |
| Intermediate | 90 | 84.40% | 3.30% | 7.78% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100128986 | T -> G | LOC_Os01g01270.1 | missense_variant ; p.Thr1251Pro; MODERATE | nonsynonymous_codon ; T1251P | Average:43.581; most accessible tissue: Minghui63 young leaf, score: 62.741 | benign  |
-0.76 |
TOLERATED | 1.00 |
| vg0100128986 | T -> DEL | LOC_Os01g01270.1 | N | frameshift_variant | Average:43.581; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100128986 | NA | 5.31E-10 | mr1662 | 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 |
| vg0100128986 | 1.83E-06 | NA | mr1047_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 |
| vg0100128986 | NA | 3.43E-07 | mr1265_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 |
| vg0100128986 | NA | 4.73E-07 | mr1528_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 |
| vg0100128986 | 1.75E-06 | NA | mr1718_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 |
| vg0100128986 | NA | 1.92E-06 | mr1815_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 |