Search for Variation information by Variation ID:
Detailed information for vg0622507208:
| Variant ID: vg0622507208 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 22507208 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 124. )
Flanking Sequence (100 bp) in Reference Genome:
GGCTGGGGATCGTGTGACCGATGTGCTGTCATGCATTCATCCACCTTCCGGGCCACCTCCTCTTGCATGCTGAGCTCGTAGCTCGATACCCTGTACTCAA[T/G]
ATCTGCAATCTTCGCCTCGGTATCTCTCTTGCTCCTCATCCGACTCCTATACGTGTGGATGTCCTCCTTGAATCCCATCTTCCAGGGAATCACGCCTTTC
Reverse complement sequence
GAAAGGCGTGATTCCCTGGAAGATGGGATTCAAGGAGGACATCCACACGTATAGGAGTCGGATGAGGAGCAAGAGAGATACCGAGGCGAAGATTGCAGAT[A/C]
TTGAGTACAGGGTATCGAGCTACGAGCTCAGCATGCAAGAGGAGGTGGCCCGGAAGGTGGATGAATGCATGACAGCACATCGGTCACACGATCCCCAGCC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.60% | 0.20% | 35.38% | 51.76% | NA |
| All Indica | 2759 | 3.90% | 0.30% | 38.82% | 57.01% | NA |
| All Japonica | 1512 | 29.00% | 0.10% | 22.35% | 48.48% | NA |
| Aus | 269 | 6.70% | 0.40% | 68.40% | 24.54% | NA |
| Indica I | 595 | 2.20% | 0.20% | 15.29% | 82.35% | NA |
| Indica II | 465 | 3.90% | 0.20% | 29.25% | 66.67% | NA |
| Indica III | 913 | 5.70% | 0.10% | 62.98% | 31.22% | NA |
| Indica Intermediate | 786 | 3.10% | 0.60% | 34.22% | 62.09% | NA |
| Temperate Japonica | 767 | 51.00% | 0.10% | 14.47% | 34.42% | NA |
| Tropical Japonica | 504 | 4.80% | 0.20% | 32.34% | 62.70% | NA |
| Japonica Intermediate | 241 | 10.00% | 0.00% | 26.56% | 63.49% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 46.88% | 36.46% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 37.78% | 43.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0622507208 | T -> G | LOC_Os06g38062.1 | missense_variant ; p.Ile364Leu; MODERATE | nonsynonymous_codon ; I364L | Average:15.062; most accessible tissue: Minghui63 flag leaf, score: 21.194 | possibly damaging  |
-1.64 |
TOLERATED | 1.00 |
| vg0622507208 | T -> DEL | LOC_Os06g38062.1 | N | frameshift_variant | Average:15.062; most accessible tissue: Minghui63 flag leaf, score: 21.194 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0622507208 | NA | 1.63E-06 | mr1182 | 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 |
| vg0622507208 | NA | 5.03E-07 | mr1057_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 |
| vg0622507208 | NA | 5.29E-06 | mr1057_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 |
| vg0622507208 | 1.35E-06 | NA | mr1168_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 |