Search for Variation information by Variation ID:
Detailed information for vg1010619124:
| Variant ID: vg1010619124 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 10619124 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TACGTCCGAAATCGTGCACATCCAGAGGGATCAATGGTTGAGGGTTATAGTACTGAAGAGGTTGTCGAGTGCTGTATTGATTACCTTAAAGATGGATATG[C/T]
AATTGGAGTACCTGTGCCCCGACATGAGGGCAGATTGAGTGGCAGGGGAACGATAGGAAAGAAGAGATTCGTCACCCATGGTCACAAATCATTCCAAGAA
Reverse complement sequence
TTCTTGGAATGATTTGTGACCATGGGTGACGAATCTCTTCTTTCCTATCGTTCCCCTGCCACTCAATCTGCCCTCATGTCGGGGCACAGGTACTCCAATT[G/A]
CATATCCATCTTTAAGGTAATCAATACAGCACTCGACAACCTCTTCAGTACTATAACCCTCAACCATTGATCCCTCTGGATGTGCACGATTTCGGACGTA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.30% | 0.70% | 3.28% | 10.66% | NA |
| All Indica | 2759 | 84.30% | 1.20% | 1.09% | 13.34% | NA |
| All Japonica | 1512 | 84.50% | 0.00% | 7.94% | 7.61% | NA |
| Aus | 269 | 96.70% | 0.00% | 0.00% | 3.35% | NA |
| Indica I | 595 | 79.70% | 0.50% | 2.02% | 17.82% | NA |
| Indica II | 465 | 81.10% | 2.60% | 0.65% | 15.70% | NA |
| Indica III | 913 | 89.20% | 1.20% | 0.66% | 8.98% | NA |
| Indica Intermediate | 786 | 84.20% | 1.00% | 1.15% | 13.61% | NA |
| Temperate Japonica | 767 | 87.90% | 0.00% | 9.39% | 2.74% | NA |
| Tropical Japonica | 504 | 81.20% | 0.00% | 5.56% | 13.29% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 8.30% | 11.20% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 2.08% | 6.25% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 3.33% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1010619124 | C -> T | LOC_Os10g20970.1 | missense_variant ; p.Ala749Val; MODERATE | nonsynonymous_codon ; A749V | Average:15.858; most accessible tissue: Minghui63 panicle, score: 25.313 | possibly damaging  |
1.565 |
DELETERIOUS | 0.01 |
| vg1010619124 | C -> DEL | LOC_Os10g20970.1 | N | frameshift_variant | Average:15.858; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1010619124 | 3.88E-06 | 3.88E-06 | mr1392 | 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 |