Search for Variation information by Variation ID:
Detailed information for vg1020503467:
| Variant ID: vg1020503467 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 20503467 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.32, others allele: 0.00, population size: 28. )
Flanking Sequence (100 bp) in Reference Genome:
TTTTGGTGAGGGTCACCACGTCGCTCAGCTTCGTGACCTCGCCCGCTTCCTTGGCTTCTCGTGTCCTGAGTACACGGGGTACTCTGTGGACCGTGTTCCC[T/C]
CTCGTTATGAGCTTTCGGTGTACCTTTACCCTCGTGGAGGTATACACGGGGCTGGCCTTCGCCCACACCACTTCACTGTGGCCAGGCCCACTCTCCAGAT
Reverse complement sequence
ATCTGGAGAGTGGGCCTGGCCACAGTGAAGTGGTGTGGGCGAAGGCCAGCCCCGTGTATACCTCCACGAGGGTAAAGGTACACCGAAAGCTCATAACGAG[A/G]
GGGAACACGGTCCACAGAGTACCCCGTGTACTCAGGACACGAGAAGCCAAGGAAGCGGGCGAGGTCACGAAGCTGAGCGACGTGGTGACCCTCACCAAAA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.80% | 19.00% | 3.85% | 49.39% | NA |
| All Indica | 2759 | 7.60% | 9.90% | 6.16% | 76.37% | NA |
| All Japonica | 1512 | 62.50% | 29.80% | 0.20% | 7.54% | NA |
| Aus | 269 | 43.90% | 47.60% | 1.12% | 7.43% | NA |
| Indica I | 595 | 17.80% | 2.40% | 6.55% | 73.28% | NA |
| Indica II | 465 | 6.20% | 1.90% | 3.87% | 87.96% | NA |
| Indica III | 913 | 2.10% | 18.30% | 7.34% | 72.29% | NA |
| Indica Intermediate | 786 | 7.10% | 10.40% | 5.85% | 76.59% | NA |
| Temperate Japonica | 767 | 86.70% | 11.20% | 0.00% | 2.09% | NA |
| Tropical Japonica | 504 | 21.60% | 60.90% | 0.60% | 16.87% | NA |
| Japonica Intermediate | 241 | 71.00% | 23.70% | 0.00% | 5.39% | NA |
| VI/Aromatic | 96 | 8.30% | 31.20% | 2.08% | 58.33% | NA |
| Intermediate | 90 | 34.40% | 20.00% | 4.44% | 41.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1020503467 | T -> C | LOC_Os10g38370.1 | missense_variant ; p.Ser79Pro; MODERATE | nonsynonymous_codon ; S79P | Average:13.862; most accessible tissue: Callus, score: 25.312 | possibly damaging  |
-1.531 |
TOLERATED | 1.00 |
| vg1020503467 | T -> DEL | LOC_Os10g38370.1 | N | frameshift_variant | Average:13.862; most accessible tissue: Callus, score: 25.312 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1020503467 | 4.54E-06 | 4.53E-06 | mr1313 | 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 |
| vg1020503467 | 3.08E-06 | 3.07E-06 | mr1473 | 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 |
| vg1020503467 | 1.26E-07 | 1.26E-07 | mr1664 | 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 |