Search for Variation information by Variation ID:
Detailed information for vg0706528880:
| Variant ID: vg0706528880 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 6528880 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTATGACGCGATTGAGCCACACGCAATCTTTCTTGAATGATTTTCACCTTTTCTTCTACTTCCCTTAGGATATCCGTCCCGAAAACCTGACGTTCTCCC[G/A]
TTTGATCCCACAGAAGCGGAGTGCGGCACTTCCGACCATACAGTGCTTCGTAAGGAGCCATCTGAAGACTAGATTGATAACTGTTGTTGTATGAAAATTC
Reverse complement sequence
GAATTTTCATACAACAACAGTTATCAATCTAGTCTTCAGATGGCTCCTTACGAAGCACTGTATGGTCGGAAGTGCCGCACTCCGCTTCTGTGGGATCAAA[C/T]
GGGAGAACGTCAGGTTTTCGGGACGGATATCCTAAGGGAAGTAGAAGAAAAGGTGAAAATCATTCAAGAAAGATTGCGTGTGGCTCAATCGCGTCATAAG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.90% | 2.80% | 14.24% | 7.05% | NA |
| All Indica | 2759 | 59.80% | 4.70% | 23.70% | 11.74% | NA |
| All Japonica | 1512 | 99.60% | 0.10% | 0.07% | 0.20% | NA |
| Aus | 269 | 95.50% | 0.00% | 3.35% | 1.12% | NA |
| Indica I | 595 | 69.60% | 5.90% | 11.60% | 12.94% | NA |
| Indica II | 465 | 71.00% | 1.90% | 12.90% | 14.19% | NA |
| Indica III | 913 | 43.30% | 6.40% | 39.76% | 10.62% | NA |
| Indica Intermediate | 786 | 65.00% | 3.70% | 20.61% | 10.69% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 10.00% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0706528880 | G -> DEL | LOC_Os07g11800.1 | N | frameshift_variant | Average:21.985; most accessible tissue: Zhenshan97 root, score: 36.298 | N | N | N | N |
| vg0706528880 | G -> A | LOC_Os07g11800.1 | missense_variant ; p.Thr1181Met; MODERATE | nonsynonymous_codon ; T1181M | Average:21.985; most accessible tissue: Zhenshan97 root, score: 36.298 | probably damaging  |
2.46 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0706528880 | 2.41E-06 | 3.90E-06 | mr1547 | 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 |
| vg0706528880 | NA | 5.32E-06 | mr1547 | 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 |
| vg0706528880 | 1.36E-06 | 5.18E-07 | mr1743 | 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 |
| vg0706528880 | 4.60E-06 | 4.14E-07 | mr1743 | 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 |
| vg0706528880 | 4.75E-06 | NA | mr1709_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 |