Search for Variation information by Variation ID:
Detailed information for vg1000477627:
| Variant ID: vg1000477627 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 477627 |
| Reference Allele: G | Alternative Allele: A,GTGTCTATCC |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 90. )
Flanking Sequence (100 bp) in Reference Genome:
TGAGGATCCCTCTCCTCTCTCAAACCGCGTTTTAGTAACCCTGTATTGCTCTGGTAGTTCAAGCTGCACAACACGGCTAGGTGGAGTTAGCACCCTTCTG[G/A,GTGTCTATCC]
TGTCTATCCATTCTCTGTATTGACATCTCCTTGGTGGTTCCTGGGAGAAAAGAATAGATGTGAAGCGAGCAAAGTTAGTAAATGTTGTGAGAAAATAAGG
Reverse complement sequence
CCTTATTTTCTCACAACATTTACTAACTTTGCTCGCTTCACATCTATTCTTTTCTCCCAGGAACCACCAAGGAGATGTCAATACAGAGAATGGATAGACA[C/T,GGATAGACAC]
CAGAAGGGTGCTAACTCCACCTAGCCGTGTTGTGCAGCTTGAACTACCAGAGCAATACAGGGTTACTAAAACGCGGTTTGAGAGAGGAGAGGGATCCTCA
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 | 74.40% | 15.20% | 0.30% | 7.32% | GTGTCTATCC: 2.84% |
| All Indica | 2759 | 69.90% | 25.80% | 0.29% | 3.66% | GTGTCTATCC: 0.36% |
| All Japonica | 1512 | 97.90% | 0.10% | 0.07% | 0.53% | GTGTCTATCC: 1.39% |
| Aus | 269 | 7.80% | 0.70% | 1.12% | 69.52% | GTGTCTATCC: 20.82% |
| Indica I | 595 | 57.30% | 42.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 94.80% | 4.30% | 0.00% | 0.86% | NA |
| Indica III | 913 | 67.90% | 25.60% | 0.55% | 5.70% | GTGTCTATCC: 0.22% |
| Indica Intermediate | 786 | 67.00% | 25.80% | 0.38% | 5.73% | GTGTCTATCC: 1.02% |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.00% | GTGTCTATCC: 0.60% |
| Japonica Intermediate | 241 | 89.20% | 0.00% | 0.41% | 2.90% | GTGTCTATCC: 7.47% |
| VI/Aromatic | 96 | 13.50% | 1.00% | 0.00% | 42.71% | GTGTCTATCC: 42.71% |
| Intermediate | 90 | 77.80% | 3.30% | 2.22% | 10.00% | GTGTCTATCC: 6.67% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000477627 | G -> GTGTCTATCC | LOC_Os10g01740.1 | inframe_insertion ; p.Asp14_Thr15insArgIleAsp; MODERATE | inframe_variant | Average:19.947; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1000477627 | G -> A | LOC_Os10g01740.1 | missense_variant ; p.Thr15Ile; MODERATE | nonsynonymous_codon ; T15I | Average:19.947; most accessible tissue: Minghui63 panicle, score: 29.741 | benign  |
0.472 |
DELETERIOUS | 0.00 |
| vg1000477627 | G -> DEL | LOC_Os10g01740.1 | N | frameshift_variant | Average:19.947; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000477627 | NA | 1.54E-06 | mr1655_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 |