Search for Variation information by Variation ID:
Detailed information for vg0810825523:
| Variant ID: vg0810825523 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 10825523 |
| Reference Allele: GATTCCAACCTTTTAGATTTTTCAATCTCAA | Alternative Allele: G,TATTCCAACCTTTTAGATTTTTCAATCTCAA |
| Primary Allele: GATTCCAACCTTTTAGATTT TTCAATCTCAA | Secondary Allele: TATTCCAACCTTTTAGATTT TTCAATCTCAA |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACTTGCACAAAAAGCAACTTTGTATTTTTTCAAAACATTCTTTGTCAAAATCAACTCATCAACAACATGAGCATGTAAAGCAAATCCAAGAGCAAAAGAA[GATTCCAACCTTTTAGATTTTTCAATCTCAA/G,TATTCCAACCTTTTAGATTTTTCAATCTCAA]
ATTCCAATTTTTTGCAATTAACAGAATTGACATCTCGCAAAGCATTAATTTCAGAAAATAAAACTTCACAAGATTGACAATTATCATCATCAGGAATCGA
Reverse complement sequence
TCGATTCCTGATGATGATAATTGTCAATCTTGTGAAGTTTTATTTTCTGAAATTAATGCTTTGCGAGATGTCAATTCTGTTAATTGCAAAAAATTGGAAT[TTGAGATTGAAAAATCTAAAAGGTTGGAATC/C,TTGAGATTGAAAAATCTAAAAGGTTGGAATA]
TTCTTTTGCTCTTGGATTTGCTTTACATGCTCATGTTGTTGATGAGTTGATTTTGACAAAGAATGTTTTGAAAAAATACAAAGTTGCTTTTTGTGCAAGT
Allele Frequencies:
| Populations | Population Size | Frequency of GATTCCAACCTTTTAGATTT TTCAATCTCAA(primary allele) | Frequency of TATTCCAACCTTTTAGATTT TTCAATCTCAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.00% | 0.20% | 0.15% | 1.61% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 94.40% | 0.70% | 0.33% | 4.63% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.80% | 0.30% | 0.13% | 0.78% | NA |
| Tropical Japonica | 504 | 91.70% | 0.60% | 0.60% | 7.14% | NA |
| Japonica Intermediate | 241 | 85.90% | 2.10% | 0.41% | 11.62% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 2.08% | 5.21% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0810825523 | GATTCCAACCTTTTAGATTTTTCAATCTCAA -> G | LOC_Os08g17690.1 | disruptive_inframe_deletion ; p.Phe202_Glu211del; MODERATE | N | Average:14.914; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |
| vg0810825523 | GATTCCAACCTTTTAGATTTTTCAATCTCAA -> TATTCCAACCTTTTAGATTTTTCAATCTCA A | LOC_Os08g17690.1 | missense_variant ; p.Ser212Tyr; MODERATE | nonsynonymous_codon ; S212Y | Average:14.914; most accessible tissue: Zhenshan97 root, score: 30.989 | probably damaging  |
+2.283 |
N | N |
| vg0810825523 | GATTCCAACCTTTTAGATTTTTCAATCTCAA -> DEL | LOC_Os08g17690.1 | N | frameshift_variant | Average:14.914; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0810825523 | NA | 3.64E-11 | mr1084 | 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 |
| vg0810825523 | NA | 7.75E-10 | mr1206 | 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 |
| vg0810825523 | NA | 5.73E-08 | mr1405 | 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 |
| vg0810825523 | NA | 5.95E-06 | mr1405 | 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 |
| vg0810825523 | NA | 3.32E-07 | mr1668 | 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 |
| vg0810825523 | NA | 1.94E-06 | mr1880 | 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 |
| vg0810825523 | NA | 5.28E-10 | mr1905_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 |