Search for Variation information by Variation ID:
Detailed information for vg0404932550:
| Variant ID: vg0404932550 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4932550 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.21, others allele: 0.00, population size: 68. )
Flanking Sequence (100 bp) in Reference Genome:
AGATGAGTGAAACCACCGGTAGCCCTTTTGAATGGGCCGACCATGTCGAGCCCCCAAACGGCGAACGACCAGGATAACGGGATGGTTTGCAACTCCTGAG[T/C]
TGGTAAATGAGTCTGTCGGGCAAAAAATTGACAACCTTCGCATGTTCGCACAATTTTATCGGCGTCGGATACCGCAGTAGGCCAGAAAAAACCCTGCCGA
Reverse complement sequence
TCGGCAGGGTTTTTTCTGGCCTACTGCGGTATCCGACGCCGATAAAATTGTGCGAACATGCGAAGGTTGTCAATTTTTTGCCCGACAGACTCATTTACCA[A/G]
CTCAGGAGTTGCAAACCATCCCGTTATCCTGGTCGTTCGCCGTTTGGGGGCTCGACATGGTCGGCCCATTCAAAAGGGCTACCGGTGGTTTCACTCATCT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.70% | 27.30% | 0.30% | 5.76% | NA |
| All Indica | 2759 | 92.10% | 6.40% | 0.25% | 1.20% | NA |
| All Japonica | 1512 | 13.50% | 70.60% | 0.40% | 15.48% | NA |
| Aus | 269 | 96.70% | 3.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 94.50% | 4.50% | 0.17% | 0.84% | NA |
| Indica II | 465 | 86.90% | 11.80% | 0.22% | 1.08% | NA |
| Indica III | 913 | 94.70% | 3.50% | 0.44% | 1.31% | NA |
| Indica Intermediate | 786 | 90.50% | 8.00% | 0.13% | 1.40% | NA |
| Temperate Japonica | 767 | 4.30% | 88.00% | 0.13% | 7.56% | NA |
| Tropical Japonica | 504 | 24.20% | 53.60% | 0.60% | 21.63% | NA |
| Japonica Intermediate | 241 | 20.30% | 51.00% | 0.83% | 27.80% | NA |
| VI/Aromatic | 96 | 86.50% | 13.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 26.70% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0404932550 | T -> C | LOC_Os04g09284.1 | missense_variant ; p.Thr1295Ala; MODERATE | nonsynonymous_codon ; T1295A | Average:28.258; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | benign  |
-1.211 |
TOLERATED | 1.00 |
| vg0404932550 | T -> DEL | LOC_Os04g09284.1 | N | frameshift_variant | Average:28.258; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0404932550 | NA | 1.93E-16 | mr1035 | 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 |
| vg0404932550 | NA | 3.59E-07 | mr1510 | 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 |
| vg0404932550 | 2.62E-06 | NA | mr1611 | 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 |
| vg0404932550 | NA | 9.77E-27 | mr1617 | 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 |
| vg0404932550 | NA | 9.35E-14 | mr1626 | 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 |
| vg0404932550 | NA | 2.48E-09 | mr1637 | 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 |
| vg0404932550 | NA | 1.29E-07 | mr1804 | 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 |
| vg0404932550 | NA | 8.12E-15 | mr1035_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 |