Search for Variation information by Variation ID:
Detailed information for vg0223426765:
| Variant ID: vg0223426765 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 23426765 |
| Reference Allele: GCCAACGCCAAC | Alternative Allele: TCCAACGCCAAC,G |
| Primary Allele: TCCAACGCCAAC | Secondary Allele: GCCAACGCCAAC |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CATCTGCCGCTCTGGATCCCAAGCTTGCTCCTCTGCTGCTGTTCGGCCACGGCGACGCCACGTTCCTGTACAGCGTGCCGAAGAGAGCGCTGCTGCCAAT[GCCAACGCCAAC/TCCAACGCCAAC,G]
GAGGGTGGGCGACGGCGGCGTCGACGACATGATGAGAGGCCACCGCTGGTGGACCACGGCGCAGGGCTGGTTGCTCATGGCGCGCCGCGGCTCGCCGTGC
Reverse complement sequence
GCACGGCGAGCCGCGGCGCGCCATGAGCAACCAGCCCTGCGCCGTGGTCCACCAGCGGTGGCCTCTCATCATGTCGTCGACGCCGCCGTCGCCCACCCTC[GTTGGCGTTGGC/GTTGGCGTTGGA,C]
ATTGGCAGCAGCGCTCTCTTCGGCACGCTGTACAGGAACGTGGCGTCGCCGTGGCCGAACAGCAGCAGAGGAGCAAGCTTGGGATCCAGAGCGGCAGATG
Allele Frequencies:
| Populations | Population Size | Frequency of TCCAACGCCAAC(primary allele) | Frequency of GCCAACGCCAAC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.00% | 26.80% | 1.59% | 31.65% | G: 0.02% |
| All Indica | 2759 | 53.40% | 4.70% | 2.46% | 39.40% | NA |
| All Japonica | 1512 | 4.70% | 71.40% | 0.33% | 23.54% | G: 0.07% |
| Aus | 269 | 98.10% | 1.50% | 0.00% | 0.37% | NA |
| Indica I | 595 | 35.30% | 7.60% | 4.54% | 52.61% | NA |
| Indica II | 465 | 60.40% | 4.10% | 2.15% | 33.33% | NA |
| Indica III | 913 | 54.50% | 2.40% | 1.75% | 41.29% | NA |
| Indica Intermediate | 786 | 61.70% | 5.60% | 1.91% | 30.79% | NA |
| Temperate Japonica | 767 | 2.10% | 79.90% | 0.13% | 17.86% | NA |
| Tropical Japonica | 504 | 9.10% | 57.50% | 0.79% | 32.34% | G: 0.20% |
| Japonica Intermediate | 241 | 3.70% | 73.00% | 0.00% | 23.24% | NA |
| VI/Aromatic | 96 | 59.40% | 11.50% | 1.04% | 28.12% | NA |
| Intermediate | 90 | 25.60% | 45.60% | 1.11% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0223426765 | GCCAACGCCAAC -> G | LOC_Os02g38770.1 | frameshift_variant ; p.Pro41fs; HIGH | frameshift_variant | Average:17.628; most accessible tissue: Callus, score: 54.872 | N | N | N | N |
| vg0223426765 | GCCAACGCCAAC -> TCCAACGCCAAC | LOC_Os02g38770.1 | missense_variant ; p.Met40Ile; MODERATE | nonsynonymous_codon ; M40I | Average:17.628; most accessible tissue: Callus, score: 54.872 | benign  |
-0.325 |
N | N |
| vg0223426765 | GCCAACGCCAAC -> DEL | LOC_Os02g38770.1 | N | frameshift_variant | Average:17.628; most accessible tissue: Callus, score: 54.872 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0223426765 | NA | 3.43E-06 | mr1709 | 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 |
| vg0223426765 | NA | 5.34E-13 | mr1740 | 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 |
| vg0223426765 | NA | 8.55E-06 | mr1882 | 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 |
| vg0223426765 | 1.51E-07 | 1.51E-07 | mr1440_2 | Jap_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 |