Search for Variation information by Variation ID:
Detailed information for vg0319643905:
| Variant ID: vg0319643905 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 19643905 |
| Reference Allele: G | Alternative Allele: C,GTT,T |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, C: 0.05, others allele: 0.00, population size: 93. )
Flanking Sequence (100 bp) in Reference Genome:
TCATGGCCTGATGACGTTCTGGGTAGACCAGTGATGAAATCCATACCGATTTCCTCCCACTTCCATTCTGGTATCTTCAAAGGCTGCAACAACCCGGCGG[G/C,GTT,T]
TTTCTGATGTTCTGCCTTGACCTGCTGGCAAACATCACACACAGCTTCATATTCCGCTATCTCACGCTTCATACTTGCCCACCAAAATCTTTCCTTGAGA
Reverse complement sequence
TCTCAAGGAAAGATTTTGGTGGGCAAGTATGAAGCGTGAGATAGCGGAATATGAAGCTGTGTGTGATGTTTGCCAGCAGGTCAAGGCAGAACATCAGAAA[C/G,AAC,A]
CCGCCGGGTTGTTGCAGCCTTTGAAGATACCAGAATGGAAGTGGGAGGAAATCGGTATGGATTTCATCACTGGTCTACCCAGAACGTCATCAGGCCATGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.10% | 18.50% | 10.03% | 1.63% | GTT: 2.35%; T: 1.42% |
| All Indica | 2759 | 53.00% | 30.60% | 13.59% | 0.72% | T: 1.78%; GTT: 0.36% |
| All Japonica | 1512 | 83.50% | 0.00% | 5.36% | 3.64% | GTT: 6.55%; T: 0.93% |
| Aus | 269 | 87.40% | 8.90% | 3.35% | 0.37% | NA |
| Indica I | 595 | 62.70% | 29.60% | 6.89% | 0.50% | T: 0.17%; GTT: 0.17% |
| Indica II | 465 | 75.10% | 12.90% | 10.75% | 0.65% | GTT: 0.43%; T: 0.22% |
| Indica III | 913 | 25.40% | 49.10% | 20.59% | 0.77% | T: 3.83%; GTT: 0.33% |
| Indica Intermediate | 786 | 64.60% | 20.20% | 12.21% | 0.89% | T: 1.53%; GTT: 0.51% |
| Temperate Japonica | 767 | 96.60% | 0.00% | 0.91% | 2.35% | GTT: 0.13% |
| Tropical Japonica | 504 | 65.70% | 0.00% | 9.72% | 4.96% | GTT: 17.06%; T: 2.58% |
| Japonica Intermediate | 241 | 79.30% | 0.00% | 10.37% | 4.98% | GTT: 4.98%; T: 0.41% |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 0.00% | T: 2.08% |
| Intermediate | 90 | 80.00% | 6.70% | 7.78% | 1.11% | T: 2.22%; GTT: 2.22% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319643905 | G -> C | LOC_Os03g35430.1 | missense_variant ; p.Pro1061Ala; MODERATE | nonsynonymous_codon ; P1061A | Average:31.209; most accessible tissue: Minghui63 young leaf, score: 63.571 | benign  |
1.223 |
DELETERIOUS | 0.00 |
| vg0319643905 | G -> DEL | LOC_Os03g35430.1 | N | frameshift_variant | Average:31.209; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |
| vg0319643905 | G -> GTT | LOC_Os03g35430.1 | frameshift_variant ; p.Pro1061fs; HIGH | frameshift_variant | Average:31.209; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |
| vg0319643905 | G -> T | LOC_Os03g35430.1 | missense_variant ; p.Pro1061Thr; MODERATE | nonsynonymous_codon ; P1061T | Average:31.209; most accessible tissue: Minghui63 young leaf, score: 63.571 | possibly damaging |
1.567 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0319643905 | NA | 3.69E-07 | mr1570 | Ind_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 |
| vg0319643905 | 2.03E-07 | 1.45E-10 | mr1570_2 | Ind_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 |