Search for Variation information by Variation ID:
Detailed information for vg0620617222:
| Variant ID: vg0620617222 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20617222 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCCTCGACTCCAACGATTTTCCTCTTGCCTGGGAGAACAACATGGCGTCTTGGCTCATCGGGCCCTTTCCCCTTCTTTGGTTTGCTATCCATGTCCTTCA[C/T]
GTAAAAAACTTGTATTACATCATTGGCTAGAACGAATGGTTCATCTGAGTATCCTACCTTATTTAAGTCAACCGTTGTCATCCCGCTGTCATCAATCGTT
Reverse complement sequence
AACGATTGATGACAGCGGGATGACAACGGTTGACTTAAATAAGGTAGGATACTCAGATGAACCATTCGTTCTAGCCAATGATGTAATACAAGTTTTTTAC[G/A]
TGAAGGACATGGATAGCAAACCAAAGAAGGGGAAAGGGCCCGATGAGCCAAGACGCCATGTTGTTCTCCCAGGCAAGAGGAAAATCGTTGGAGTCGAGGA
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 | 16.90% | 15.90% | 10.79% | 56.37% | NA |
| All Indica | 2759 | 1.40% | 1.20% | 9.21% | 88.18% | NA |
| All Japonica | 1512 | 48.70% | 42.50% | 3.70% | 5.16% | NA |
| Aus | 269 | 1.90% | 0.00% | 60.59% | 37.55% | NA |
| Indica I | 595 | 1.50% | 0.20% | 3.87% | 94.45% | NA |
| Indica II | 465 | 0.90% | 2.60% | 6.24% | 90.32% | NA |
| Indica III | 913 | 1.40% | 0.30% | 12.81% | 85.43% | NA |
| Indica Intermediate | 786 | 1.80% | 2.00% | 10.81% | 85.37% | NA |
| Temperate Japonica | 767 | 78.10% | 18.10% | 0.26% | 3.52% | NA |
| Tropical Japonica | 504 | 5.00% | 79.40% | 8.33% | 7.34% | NA |
| Japonica Intermediate | 241 | 46.50% | 42.70% | 4.98% | 5.81% | NA |
| VI/Aromatic | 96 | 1.00% | 52.10% | 28.12% | 18.75% | NA |
| Intermediate | 90 | 21.10% | 30.00% | 11.11% | 37.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620617222 | C -> T | LOC_Os06g35360.1 | missense_variant ; p.Val892Met; MODERATE | nonsynonymous_codon ; V892M | Average:11.328; most accessible tissue: Zhenshan97 panicle, score: 24.575 | benign  |
1.224 |
DELETERIOUS | 0.03 |
| vg0620617222 | C -> DEL | LOC_Os06g35360.1 | N | frameshift_variant | Average:11.328; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0620617222 | 3.21E-07 | NA | mr1347_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 |
| vg0620617222 | NA | 6.65E-08 | mr1347_2 | Jap_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 |
| vg0620617222 | NA | 6.48E-10 | mr1398_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 |
| vg0620617222 | NA | 3.83E-07 | mr1966_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 |