Search for Variation information by Variation ID:
Detailed information for vg1124028416:
| Variant ID: vg1124028416 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24028416 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AACAATCGCTGTACACAGTGGCGCAGTTCGAAATCGAACCACCAGCCTGCTGGGTCCACTCGGAGAAGTCGAAGGCCGAGGCATCTTCGGCAGGGACCCC[G/T]
CTCACCTTTGCACCCATGTCAGTAATGGCGAGGCGGAGAGTTTGGCACGCCGTTCTCGCGGATTCGGTGGTTTTTGCCATCTCCCGCGAAAACCGCTGCG
Reverse complement sequence
CGCAGCGGTTTTCGCGGGAGATGGCAAAAACCACCGAATCCGCGAGAACGGCGTGCCAAACTCTCCGCCTCGCCATTACTGACATGGGTGCAAAGGTGAG[C/A]
GGGGTCCCTGCCGAAGATGCCTCGGCCTTCGACTTCTCCGAGTGGACCCAGCAGGCTGGTGGTTCGATTTCGAACTGCGCCACTGTGTACAGCGATTGTT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.00% | 27.80% | 6.64% | 33.50% | NA |
| All Indica | 2759 | 24.50% | 40.70% | 10.22% | 24.57% | NA |
| All Japonica | 1512 | 46.40% | 2.10% | 0.86% | 50.60% | NA |
| Aus | 269 | 32.70% | 51.70% | 3.35% | 12.27% | NA |
| Indica I | 595 | 14.30% | 32.10% | 8.74% | 44.87% | NA |
| Indica II | 465 | 28.40% | 24.10% | 16.13% | 31.40% | NA |
| Indica III | 913 | 23.40% | 58.20% | 8.65% | 9.75% | NA |
| Indica Intermediate | 786 | 31.20% | 36.80% | 9.67% | 22.39% | NA |
| Temperate Japonica | 767 | 60.10% | 3.30% | 1.30% | 35.33% | NA |
| Tropical Japonica | 504 | 38.30% | 0.20% | 0.20% | 61.31% | NA |
| Japonica Intermediate | 241 | 19.90% | 2.50% | 0.83% | 76.76% | NA |
| VI/Aromatic | 96 | 10.40% | 6.20% | 2.08% | 81.25% | NA |
| Intermediate | 90 | 42.20% | 16.70% | 8.89% | 32.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1124028416 | G -> T | LOC_Os11g40300.1 | missense_variant ; p.Ser543Arg; MODERATE | stop_gained | Average:15.572; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| vg1124028416 | G -> T | LOC_Os11g40300.1 | missense_variant ; p.Ser543Arg; MODERATE | nonsynonymous_codon ; S543R | Average:15.572; most accessible tissue: Minghui63 panicle, score: 50.413 | possibly damaging  |
-1.888 |
TOLERATED | 1.00 |
| vg1124028416 | G -> DEL | LOC_Os11g40300.1 | N | frameshift_variant | Average:15.572; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124028416 | NA | 7.88E-06 | mr1153_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 |
| vg1124028416 | NA | 1.25E-06 | mr1363_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 |
| vg1124028416 | NA | 7.64E-06 | mr1407_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 |
| vg1124028416 | NA | 1.08E-06 | mr1479_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 |
| vg1124028416 | 5.91E-07 | NA | mr1608_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 |
| vg1124028416 | NA | 5.02E-06 | mr1677_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 |