Search for Variation information by Variation ID:
Detailed information for vg0720591049:
| Variant ID: vg0720591049 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 20591049 |
| Reference Allele: AAGCTCTGGTG | Alternative Allele: GAGCTCTGGTG,A |
| Primary Allele: GAGCTCTGGTG | Secondary Allele: AAGCTCTGGTG |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCCAGAACCCTGAGCCACCGTCGGAACCCCTGCGGCGCTCTTTGCCACGGTGTGGAGTGATGCCATCATCGATGGCCTGGGCCACCTCGCCCCATCAGAC[AAGCTCTGGTG/GAGCTCTGGTG,A]
GATGCTTGTCCCGGCGGCCGATGTCATTGGCATCTTCATCACCATGTTCCAGGTGATGATCTTTAGGTGCGAAGGGGTGTGCTAGGGCGCAGTGATCCAT
Reverse complement sequence
ATGGATCACTGCGCCCTAGCACACCCCTTCGCACCTAAAGATCATCACCTGGAACATGGTGATGAAGATGCCAATGACATCGGCCGCCGGGACAAGCATC[CACCAGAGCTT/CACCAGAGCTC,T]
GTCTGATGGGGCGAGGTGGCCCAGGCCATCGATGATGGCATCACTCCACACCGTGGCAAAGAGCGCCGCAGGGGTTCCGACGGTGGCTCAGGGTTCTGGC
Allele Frequencies:
| Populations | Population Size | Frequency of GAGCTCTGGTG(primary allele) | Frequency of AAGCTCTGGTG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.50% | 15.60% | 0.08% | 0.25% | A: 9.65% |
| All Indica | 2759 | 98.70% | 1.00% | 0.04% | 0.00% | A: 0.29% |
| All Japonica | 1512 | 24.50% | 45.60% | 0.20% | 0.79% | A: 28.90% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.60% | 2.20% | 0.00% | 0.00% | A: 0.22% |
| Indica III | 913 | 99.80% | 0.00% | 0.00% | 0.00% | A: 0.22% |
| Indica Intermediate | 786 | 97.20% | 2.00% | 0.13% | 0.00% | A: 0.64% |
| Temperate Japonica | 767 | 3.40% | 79.50% | 0.39% | 1.56% | A: 15.12% |
| Tropical Japonica | 504 | 60.90% | 4.80% | 0.00% | 0.00% | A: 34.33% |
| Japonica Intermediate | 241 | 15.40% | 23.20% | 0.00% | 0.00% | A: 61.41% |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 17.80% | 0.00% | 0.00% | A: 12.22% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0720591049 | AAGCTCTGGTG -> DEL | LOC_Os07g34360.1 | N | frameshift_variant | Average:67.581; most accessible tissue: Zhenshan97 young leaf, score: 86.055 | N | N | N | N |
| vg0720591049 | AAGCTCTGGTG -> A | LOC_Os07g34360.1 | frameshift_variant ; p.His16fs; HIGH | frameshift_variant | Average:67.581; most accessible tissue: Zhenshan97 young leaf, score: 86.055 | N | N | N | N |
| vg0720591049 | AAGCTCTGGTG -> GAGCTCTGGTG | LOC_Os07g34360.1 | missense_variant ; p.Leu19Ser; MODERATE | nonsynonymous_codon ; L19S | Average:67.581; most accessible tissue: Zhenshan97 young leaf, score: 86.055 | possibly damaging  |
+1.603 |
N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0720591049 | NA | 1.47E-10 | Grain_weight | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0720591049 | NA | 1.38E-26 | mr1617 | 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 |
| vg0720591049 | NA | 1.57E-37 | mr1137_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 |
| vg0720591049 | NA | 6.54E-08 | mr1137_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 |
| vg0720591049 | NA | 7.86E-31 | mr1617_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 |
| vg0720591049 | NA | 4.47E-06 | mr1617_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 |
| vg0720591049 | 2.71E-06 | NA | mr1913_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 |