Search for Variation information by Variation ID:
Detailed information for vg0206906369:
| Variant ID: vg0206906369 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 6906369 |
| Reference Allele: TTAATGA | Alternative Allele: CTAATGA,T |
| Primary Allele: T | Secondary Allele: TTAATGA |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATCCAGCGCATCATAAGGGATAGGCACATGGGAGACTCAGGCAGCAAGCCTCAGGCAAGAGTGACATGGGTGACAGGCCGTCGAAGGAACCAAGAAACAA[TTAATGA/CTAATGA,T]
TGCACCCAAGCACATTGTGAAGATACCTATCCGCAAAGATGATCAAGGCAGGTCAAAGCACTCGGCTGTGGTAATTGAACCTCTACGCGATGATCATGAT
Reverse complement sequence
ATCATGATCATCGCGTAGAGGTTCAATTACCACAGCCGAGTGCTTTGACCTGCCTTGATCATCTTTGCGGATAGGTATCTTCACAATGTGCTTGGGTGCA[TCATTAA/TCATTAG,A]
TTGTTTCTTGGTTCCTTCGACGGCCTGTCACCCATGTCACTCTTGCCTGAGGCTTGCTGCCTGAGTCTCCCATGTGCCTATCCCTTATGATGCGCTGGAT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TTAATGA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.50% | 21.70% | 9.06% | 13.16% | CTAATGA: 18.54% |
| All Indica | 2759 | 57.00% | 1.30% | 9.53% | 1.78% | CTAATGA: 30.41% |
| All Japonica | 1512 | 2.20% | 62.60% | 0.53% | 33.60% | CTAATGA: 1.06% |
| Aus | 269 | 42.00% | 0.70% | 42.75% | 14.13% | CTAATGA: 0.37% |
| Indica I | 595 | 60.20% | 2.40% | 9.58% | 1.01% | CTAATGA: 26.89% |
| Indica II | 465 | 42.60% | 2.20% | 9.68% | 1.51% | CTAATGA: 44.09% |
| Indica III | 913 | 62.30% | 0.10% | 8.43% | 1.64% | CTAATGA: 27.49% |
| Indica Intermediate | 786 | 56.90% | 1.40% | 10.69% | 2.67% | CTAATGA: 28.37% |
| Temperate Japonica | 767 | 1.30% | 89.60% | 0.26% | 8.08% | CTAATGA: 0.78% |
| Tropical Japonica | 504 | 3.60% | 30.20% | 0.79% | 64.88% | CTAATGA: 0.60% |
| Japonica Intermediate | 241 | 2.50% | 44.40% | 0.83% | 49.38% | CTAATGA: 2.90% |
| VI/Aromatic | 96 | 28.10% | 21.90% | 30.21% | 17.71% | CTAATGA: 2.08% |
| Intermediate | 90 | 31.10% | 23.30% | 14.44% | 11.11% | CTAATGA: 20.00% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206906369 | TTAATGA -> T | LOC_Os02g13040.1 | inframe_deletion ; p.Asn26_Asp27del; MODERATE | inframe_variant | Average:52.026; most accessible tissue: Zhenshan97 flag leaf, score: 81.41 | N | N | N | N |
| vg0206906369 | TTAATGA -> CTAATGA | LOC_Os02g13040.1 | missense_variant ; p.Ile25Thr; MODERATE | nonsynonymous_codon ; I25T | Average:52.026; most accessible tissue: Zhenshan97 flag leaf, score: 81.41 | benign  |
-0.184 |
N | N |
| vg0206906369 | TTAATGA -> DEL | LOC_Os02g13040.1 | N | frameshift_variant | Average:52.026; most accessible tissue: Zhenshan97 flag leaf, score: 81.41 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0206906369 | 2.41E-06 | 2.40E-06 | mr1417 | 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 |
| vg0206906369 | 2.01E-06 | 2.01E-06 | mr1890 | 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 |