Search for Variation information by Variation ID:
Detailed information for vg0707392578:
| Variant ID: vg0707392578 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 7392578 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 59. )
Flanking Sequence (100 bp) in Reference Genome:
CGAATTGCACCATACACCTTCTGCAATGCAGTAGCACCGAGAAGACCCACTGCATTCGGTCTCCACCTGAAGTAGTCATCATGAGCCTCCACACTAGCCA[C/T]
GATGCGCAAGAAGAGCTCCCTTGACATTCTGAACCTTCTCCTAAATAATTTTGCATTATATACAGGAGGATCTGCAAAATAATCAGCCACTATGCGCAAA
Reverse complement sequence
TTTGCGCATAGTGGCTGATTATTTTGCAGATCCTCCTGTATATAATGCAAAATTATTTAGGAGAAGGTTCAGAATGTCAAGGGAGCTCTTCTTGCGCATC[G/A]
TGGCTAGTGTGGAGGCTCATGATGACTACTTCAGGTGGAGACCGAATGCAGTGGGTCTTCTCGGTGCTACTGCATTGCAGAAGGTGTATGGTGCAATTCG
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 | 34.80% | 16.70% | 34.74% | 13.73% | NA |
| All Indica | 2759 | 6.30% | 22.00% | 55.64% | 16.06% | NA |
| All Japonica | 1512 | 79.20% | 7.40% | 3.11% | 10.32% | NA |
| Aus | 269 | 59.50% | 12.60% | 13.38% | 14.50% | NA |
| Indica I | 595 | 3.20% | 15.60% | 58.49% | 22.69% | NA |
| Indica II | 465 | 6.70% | 24.90% | 54.62% | 13.76% | NA |
| Indica III | 913 | 2.20% | 27.40% | 56.08% | 14.35% | NA |
| Indica Intermediate | 786 | 13.20% | 18.80% | 53.56% | 14.38% | NA |
| Temperate Japonica | 767 | 95.40% | 1.00% | 1.69% | 1.83% | NA |
| Tropical Japonica | 504 | 67.50% | 9.90% | 5.75% | 16.87% | NA |
| Japonica Intermediate | 241 | 51.90% | 22.40% | 2.07% | 23.65% | NA |
| VI/Aromatic | 96 | 76.00% | 22.90% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 47.80% | 14.40% | 26.67% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0707392578 | C -> DEL | LOC_Os07g12880.1 | N | frameshift_variant | Average:11.975; most accessible tissue: Callus, score: 20.292 | N | N | N | N |
| vg0707392578 | C -> T | LOC_Os07g12880.1 | missense_variant ; p.Val101Met; MODERATE | nonsynonymous_codon ; V101M | Average:11.975; most accessible tissue: Callus, score: 20.292 | probably damaging  |
2.465 |
TOLERATED | 0.22 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0707392578 | NA | 9.00E-13 | mr1031 | 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 |
| vg0707392578 | NA | 4.68E-07 | mr1040 | 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 |
| vg0707392578 | NA | 2.29E-13 | mr1056 | 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 |
| vg0707392578 | NA | 1.20E-06 | mr1058 | 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 |
| vg0707392578 | NA | 2.45E-14 | mr1362 | 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 |
| vg0707392578 | NA | 1.42E-09 | mr1379 | 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 |
| vg0707392578 | NA | 6.60E-10 | mr1581 | 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 |
| vg0707392578 | NA | 4.51E-10 | mr1836 | 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 |
| vg0707392578 | NA | 8.73E-16 | mr1457_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 |