Search for Variation information by Variation ID:
Detailed information for vg1128277188:
| Variant ID: vg1128277188 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 28277188 |
| Reference Allele: A | Alternative Allele: C,T |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGGTTGGTTGCTGAACAAGCTTCACAAAGCGAGGTTGAGTCCGCGCCGAAGAGGCGCGAAGATGACATCCTCACAAAGGCGCTCGGAACCAAAGAACATC[A/C,T]
TGGCCGGACTCGGGGAATTGGCAGCGATGTGCCCTGGAAGCATGGACTCCCGCAGTACAGCTCCCAATACAGGAAACGGAAAGTCTCCAAGGAAGAGAGG
Reverse complement sequence
CCTCTCTTCCTTGGAGACTTTCCGTTTCCTGTATTGGGAGCTGTACTGCGGGAGTCCATGCTTCCAGGGCACATCGCTGCCAATTCCCCGAGTCCGGCCA[T/G,A]
GATGTTCTTTGGTTCCGAGCGCCTTTGTGAGGATGTCATCTTCGCGCCTCTTCGGCGCGGACTCAACCTCGCTTTGTGAAGCTTGTTCAGCAACCAACCC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.80% | 17.30% | 34.51% | 27.38% | T: 0.02% |
| All Indica | 2759 | 19.10% | 27.30% | 45.78% | 7.87% | T: 0.04% |
| All Japonica | 1512 | 25.50% | 1.90% | 15.41% | 57.14% | NA |
| Aus | 269 | 16.00% | 3.70% | 13.75% | 66.54% | NA |
| Indica I | 595 | 33.40% | 25.70% | 34.79% | 6.05% | NA |
| Indica II | 465 | 10.30% | 11.60% | 63.44% | 14.62% | NA |
| Indica III | 913 | 10.70% | 42.40% | 44.14% | 2.63% | T: 0.11% |
| Indica Intermediate | 786 | 23.00% | 20.10% | 45.55% | 11.32% | NA |
| Temperate Japonica | 767 | 37.00% | 0.80% | 5.74% | 56.45% | NA |
| Tropical Japonica | 504 | 9.50% | 4.20% | 31.35% | 54.96% | NA |
| Japonica Intermediate | 241 | 22.40% | 0.80% | 12.86% | 63.90% | NA |
| VI/Aromatic | 96 | 5.20% | 14.60% | 63.54% | 16.67% | NA |
| Intermediate | 90 | 24.40% | 14.40% | 41.11% | 20.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1128277188 | A -> T | LOC_Os11g47070.1 | missense_variant ; p.His161Leu; MODERATE | nonsynonymous_codon ; H161L | Average:21.886; most accessible tissue: Zhenshan97 root, score: 34.536 | probably damaging  |
-2.34 |
TOLERATED | 0.71 |
| vg1128277188 | A -> DEL | LOC_Os11g47070.1 | N | frameshift_variant | Average:21.886; most accessible tissue: Zhenshan97 root, score: 34.536 | N | N | N | N |
| vg1128277188 | A -> C | LOC_Os11g47070.1 | missense_variant ; p.His161Pro; MODERATE | nonsynonymous_codon ; H161P | Average:21.886; most accessible tissue: Zhenshan97 root, score: 34.536 | probably damaging |
-2.329 |
TOLERATED | 0.55 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1128277188 | NA | 1.95E-09 | mr1310_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 |
| vg1128277188 | 2.03E-06 | 2.02E-06 | mr1609_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 |
| vg1128277188 | NA | 1.08E-09 | mr1959_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 |