Search for Variation information by Variation ID:
Detailed information for vg0721519373:
| Variant ID: vg0721519373 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21519373 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCCGTTCGGGTACGTCATTCCGGACTGGAGCACGTCGAGGTAGCCCGTCGTCGGGTCGTACTTCATCAGGCGGCCCGTGGAGTCGCCGGTGGCCGTGACC[A/C]
TCTCGTGCTGGGATCGCTGGAAGCGCGTGCTGCTGTCGGTGAAGTAGACCTCGCCGGTGACCTGGTTGACGTCGACGCCGTTGGTGAACTTGAACGGCAC
Reverse complement sequence
GTGCCGTTCAAGTTCACCAACGGCGTCGACGTCAACCAGGTCACCGGCGAGGTCTACTTCACCGACAGCAGCACGCGCTTCCAGCGATCCCAGCACGAGA[T/G]
GGTCACGGCCACCGGCGACTCCACGGGCCGCCTGATGAAGTACGACCCGACGACGGGCTACCTCGACGTGCTCCAGTCCGGAATGACGTACCCGAACGGC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.80% | 2.10% | 15.21% | 26.96% | NA |
| All Indica | 2759 | 40.10% | 3.00% | 19.06% | 37.80% | NA |
| All Japonica | 1512 | 80.40% | 0.70% | 9.72% | 9.19% | NA |
| Aus | 269 | 55.00% | 0.40% | 13.01% | 31.60% | NA |
| Indica I | 595 | 29.40% | 0.50% | 34.96% | 35.13% | NA |
| Indica II | 465 | 45.20% | 0.00% | 8.82% | 46.02% | NA |
| Indica III | 913 | 42.70% | 6.90% | 12.71% | 37.68% | NA |
| Indica Intermediate | 786 | 42.10% | 2.30% | 20.48% | 35.11% | NA |
| Temperate Japonica | 767 | 67.40% | 1.20% | 14.99% | 16.43% | NA |
| Tropical Japonica | 504 | 99.00% | 0.40% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 82.60% | 0.00% | 12.86% | 4.56% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 1.10% | 11.11% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721519373 | A -> DEL | LOC_Os07g35970.1 | N | frameshift_variant | Average:72.281; most accessible tissue: Minghui63 flag leaf, score: 86.468 | N | N | N | N |
| vg0721519373 | A -> C | LOC_Os07g35970.1 | missense_variant ; p.Met194Arg; MODERATE | nonsynonymous_codon ; M194R | Average:72.281; most accessible tissue: Minghui63 flag leaf, score: 86.468 | benign  |
0.232 |
TOLERATED | 0.52 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0721519373 | 1.83E-06 | NA | mr1973 | 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 |