Search for Variation information by Variation ID:
Detailed information for vg0804990899:
| Variant ID: vg0804990899 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4990899 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTTCGGCGCCAAATAGCCTCTTGGGCTAAACCACTATACAAACTAAGCTTGAGCAAAGCTCAAACTTAGCAACAGGAACAGACTTTGTCATCATATCAG[T/C]
AGGATTATCATGAGTGCTTATCTTGCATACCTTTAGCTTACCTTGCACGACTACATCGCGAACATAATGGTACTTGATATCAATGTGCTTTGTCCTCTCA
Reverse complement sequence
TGAGAGGACAAAGCACATTGATATCAAGTACCATTATGTTCGCGATGTAGTCGTGCAAGGTAAGCTAAAGGTATGCAAGATAAGCACTCATGATAATCCT[A/G]
CTGATATGATGACAAAGTCTGTTCCTGTTGCTAAGTTTGAGCTTTGCTCAAGCTTAGTTTGTATAGTGGTTTAGCCCAAGAGGCTATTTGGCGCCGAAAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.00% | 2.70% | 20.36% | 24.93% | NA |
| All Indica | 2759 | 43.90% | 1.70% | 27.55% | 26.86% | NA |
| All Japonica | 1512 | 71.40% | 0.10% | 3.90% | 24.54% | NA |
| Aus | 269 | 29.00% | 27.10% | 37.55% | 6.32% | NA |
| Indica I | 595 | 36.60% | 0.30% | 20.50% | 42.52% | NA |
| Indica II | 465 | 39.60% | 1.30% | 42.80% | 16.34% | NA |
| Indica III | 913 | 52.20% | 1.30% | 25.19% | 21.25% | NA |
| Indica Intermediate | 786 | 42.20% | 3.40% | 26.59% | 27.74% | NA |
| Temperate Japonica | 767 | 96.20% | 0.00% | 0.65% | 3.13% | NA |
| Tropical Japonica | 504 | 30.60% | 0.20% | 9.13% | 60.12% | NA |
| Japonica Intermediate | 241 | 78.00% | 0.40% | 3.32% | 18.26% | NA |
| VI/Aromatic | 96 | 41.70% | 6.20% | 26.04% | 26.04% | NA |
| Intermediate | 90 | 53.30% | 1.10% | 18.89% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804990899 | T -> C | LOC_Os08g08640.1 | missense_variant ; p.Thr1493Ala; MODERATE | nonsynonymous_codon ; T1493A | Average:12.384; most accessible tissue: Minghui63 young leaf, score: 23.613 | benign  |
-0.382 |
TOLERATED | 1.00 |
| vg0804990899 | T -> DEL | LOC_Os08g08640.1 | N | frameshift_variant | Average:12.384; most accessible tissue: Minghui63 young leaf, score: 23.613 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0804990899 | 4.80E-07 | 1.53E-07 | mr1448_2 | 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 |