Search for Variation information by Variation ID:
Detailed information for vg1218153891:
| Variant ID: vg1218153891 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18153891 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.06, others allele: 0.00, population size: 90. )
Flanking Sequence (100 bp) in Reference Genome:
CGCCTAACGCATATCTGAGTGCATCCTGTCCATTCCCCTCATTACGGCACACATGTGACCAAAGGTGGTGTCGTTCTCACCGGCTATCGGACGGAAGGTG[T/C]
TGACGTCATCGCCACTTGCTTGACGAGGGTGAAACCGGTACGCCGTGTTGCAGAAGATGTAGTTGTGGCGCTCACGAAGTCTGGCCATCATCAGGTATGC
Reverse complement sequence
GCATACCTGATGATGGCCAGACTTCGTGAGCGCCACAACTACATCTTCTGCAACACGGCGTACCGGTTTCACCCTCGTCAAGCAAGTGGCGATGACGTCA[A/G]
CACCTTCCGTCCGATAGCCGGTGAGAACGACACCACCTTTGGTCACATGTGTGCCGTAATGAGGGGAATGGACAGGATGCACTCAGATATGCGTTAGGCG
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 | 64.10% | 12.60% | 0.89% | 22.45% | NA |
| All Indica | 2759 | 46.00% | 18.00% | 1.45% | 34.58% | NA |
| All Japonica | 1512 | 98.30% | 1.30% | 0.07% | 0.33% | NA |
| Aus | 269 | 40.50% | 27.10% | 0.37% | 31.97% | NA |
| Indica I | 595 | 85.90% | 7.10% | 0.00% | 7.06% | NA |
| Indica II | 465 | 26.90% | 28.60% | 1.51% | 43.01% | NA |
| Indica III | 913 | 28.30% | 23.70% | 1.31% | 46.77% | NA |
| Indica Intermediate | 786 | 47.70% | 13.40% | 2.67% | 36.26% | NA |
| Temperate Japonica | 767 | 98.70% | 0.70% | 0.13% | 0.52% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.60% | 5.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 88.50% | 3.10% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 88.90% | 2.20% | 0.00% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218153891 | T -> C | LOC_Os12g30260.1 | missense_variant ; p.Asn164Ser; MODERATE | nonsynonymous_codon | Average:51.291; most accessible tissue: Minghui63 young leaf, score: 72.408 | benign  |
-0.257 |
TOLERATED | 1.00 |
| vg1218153891 | T -> DEL | LOC_Os12g30260.1 | N | frameshift_variant | Average:51.291; most accessible tissue: Minghui63 young leaf, score: 72.408 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218153891 | 8.74E-06 | 8.75E-06 | mr1682 | 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 |
| vg1218153891 | NA | 7.94E-06 | mr1754 | 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 |
| vg1218153891 | 3.42E-06 | NA | mr1458_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 |
| vg1218153891 | 8.13E-07 | 3.07E-08 | mr1458_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 |