Search for Variation information by Variation ID:
Detailed information for vg0110736403:
| Variant ID: vg0110736403 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 10736403 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCAAGACGCACTGTCACTCTGTACCGAGGGCCGGAACAACCGGTTGTTTTCTTTGCACCCCCAACCTCTGTCGGTAGTTCAGAACTTCATCAGATAGGAA[T/G]
GTCAGAAATCCCCATCGTCAGAGAGTTCGGAGACATGTTTCCGGAAGAACTACCAGGTATGCCGCCGAAACGAGAGATTGAGTTCCGGATAGATCTTGCT
Reverse complement sequence
AGCAAGATCTATCCGGAACTCAATCTCTCGTTTCGGCGGCATACCTGGTAGTTCTTCCGGAAACATGTCTCCGAACTCTCTGACGATGGGGATTTCTGAC[A/C]
TTCCTATCTGATGAAGTTCTGAACTACCGACAGAGGTTGGGGGTGCAAAGAAAACAACCGGTTGTTCCGGCCCTCGGTACAGAGTGACAGTGCGTCTTGC
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 | 45.60% | 4.80% | 22.24% | 27.36% | NA |
| All Indica | 2759 | 14.60% | 7.40% | 33.60% | 44.44% | NA |
| All Japonica | 1512 | 97.00% | 0.10% | 1.26% | 1.65% | NA |
| Aus | 269 | 79.60% | 4.50% | 12.64% | 3.35% | NA |
| Indica I | 595 | 12.30% | 0.30% | 21.51% | 65.88% | NA |
| Indica II | 465 | 14.00% | 5.60% | 35.91% | 44.52% | NA |
| Indica III | 913 | 13.80% | 11.90% | 39.98% | 34.28% | NA |
| Indica Intermediate | 786 | 17.60% | 8.50% | 33.97% | 39.95% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 94.80% | 0.20% | 3.17% | 1.79% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.83% | 2.07% | NA |
| VI/Aromatic | 96 | 21.90% | 7.30% | 57.29% | 13.54% | NA |
| Intermediate | 90 | 55.60% | 4.40% | 17.78% | 22.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0110736403 | T -> G | LOC_Os01g19000.1 | missense_variant ; p.Met386Arg; MODERATE | nonsynonymous_codon ; M386R | Average:7.006; most accessible tissue: Zhenshan97 young leaf, score: 17.571 | benign  |
-0.324 |
DELETERIOUS | 0.00 |
| vg0110736403 | T -> DEL | LOC_Os01g19000.1 | N | frameshift_variant | Average:7.006; most accessible tissue: Zhenshan97 young leaf, score: 17.571 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0110736403 | 2.15E-06 | 2.15E-06 | mr1197 | 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 |
| vg0110736403 | NA | 3.48E-06 | mr1310 | 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 |
| vg0110736403 | NA | 7.67E-06 | mr1679 | 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 |
| vg0110736403 | NA | 4.64E-06 | mr1693 | 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 |
| vg0110736403 | 5.75E-06 | 5.75E-06 | mr1847 | 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 |