Search for Variation information by Variation ID:
Detailed information for vg0217842756:
| Variant ID: vg0217842756 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 17842756 |
| Reference Allele: G | Alternative Allele: A,GTCA,GATCA |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 281. )
Flanking Sequence (100 bp) in Reference Genome:
TTGCTTGATGTCACTCCGCAGGGATATGACTCCTCGAGGACCAGGCATCTTCATCATCATGTAGGTATAATGCGGGACAGCCATGAACTTGGCTAACGCT[G/A,GTCA,GATCA]
GGCGTCCGAGTATGGCGTGATACGCTGTCTCGAAATCAGCGACCTTGAAACAAATGTTCTCTGTGCGGAAGTTCTCCCGAGTGCCGAAAGTAACCGGAAG
Reverse complement sequence
CTTCCGGTTACTTTCGGCACTCGGGAGAACTTCCGCACAGAGAACATTTGTTTCAAGGTCGCTGATTTCGAGACAGCGTATCACGCCATACTCGGACGCC[C/T,TGAC,TGATC]
AGCGTTAGCCAAGTTCATGGCTGTCCCGCATTATACCTACATGATGATGAAGATGCCTGGTCCTCGAGGAGTCATATCCCTGCGGAGTGACATCAAGCAA
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 | 80.00% | 9.60% | 6.54% | 3.81% | NA |
| All Indica | 2759 | 66.80% | 16.40% | 10.44% | 6.34% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Aus | 269 | 94.40% | 0.00% | 3.72% | 1.86% | NA |
| Indica I | 595 | 85.00% | 0.20% | 10.08% | 4.71% | NA |
| Indica II | 465 | 69.20% | 5.60% | 14.84% | 10.32% | NA |
| Indica III | 913 | 52.40% | 36.10% | 6.79% | 4.71% | NA |
| Indica Intermediate | 786 | 68.30% | 12.20% | 12.34% | 7.12% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 2.20% | 8.89% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0217842756 | G -> A | LOC_Os02g30040.1 | missense_variant ; p.Pro809Leu; MODERATE | nonsynonymous_codon ; P809L | Average:70.777; most accessible tissue: Minghui63 flag leaf, score: 88.798 | benign  |
1.045 |
TOLERATED | 0.08 |
| vg0217842756 | G -> GTCA | LOC_Os02g30040.1 | inframe_insertion ; p.Pro809delinsLeuThr; MODERATE | N | Average:70.777; most accessible tissue: Minghui63 flag leaf, score: 88.798 | N | N | N | N |
| vg0217842756 | G -> GTCA | LOC_Os02g30030.1 | upstream_gene_variant ; 1088.0bp to feature; MODIFIER | N | Average:70.777; most accessible tissue: Minghui63 flag leaf, score: 88.798 | N | N | N | N |
| vg0217842756 | G -> GTCA | LOC_Os02g30050.1 | upstream_gene_variant ; 3528.0bp to feature; MODIFIER | N | Average:70.777; most accessible tissue: Minghui63 flag leaf, score: 88.798 | N | N | N | N |
| vg0217842756 | G -> GTCA | LOC_Os02g30020.1 | downstream_gene_variant ; 3742.0bp to feature; MODIFIER | N | Average:70.777; most accessible tissue: Minghui63 flag leaf, score: 88.798 | N | N | N | N |
| vg0217842756 | G -> GATCA | LOC_Os02g30040.1 | frameshift_variant ; p.Pro809fs; HIGH | N | Average:70.777; most accessible tissue: Minghui63 flag leaf, score: 88.798 | N | N | N | N |
| vg0217842756 | G -> GATCA | LOC_Os02g30030.1 | upstream_gene_variant ; 1088.0bp to feature; MODIFIER | N | Average:70.777; most accessible tissue: Minghui63 flag leaf, score: 88.798 | N | N | N | N |
| vg0217842756 | G -> GATCA | LOC_Os02g30050.1 | upstream_gene_variant ; 3528.0bp to feature; MODIFIER | N | Average:70.777; most accessible tissue: Minghui63 flag leaf, score: 88.798 | N | N | N | N |
| vg0217842756 | G -> DEL | LOC_Os02g30040.1 | N | frameshift_variant | Average:70.777; most accessible tissue: Minghui63 flag leaf, score: 88.798 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0217842756 | 4.33E-06 | NA | mr1129 | 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 |
| vg0217842756 | 3.32E-06 | NA | mr1257 | 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 |
| vg0217842756 | 3.70E-06 | NA | mr1255_2 | 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 |