Search for Variation information by Variation ID:
Detailed information for vg0615088191:
| Variant ID: vg0615088191 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 15088191 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AATGTCTTCATTAACTAGTCGGCGGCGGACGAGGCAGCCGGTCGGTGAGGATGTAGACGCCCAACAACGGCGGCATAATAGGCCAGCCATGCAGGCGGAA[A/G]
CACCAGTCGGCGGCGGACGAGGCGACCGGTCGGTGAAGACGTAGACGCTCAACAACAGTGGCATAATAGGCCAGCTGTGCAGGCGGTAACACCAGTCGGT
Reverse complement sequence
ACCGACTGGTGTTACCGCCTGCACAGCTGGCCTATTATGCCACTGTTGTTGAGCGTCTACGTCTTCACCGACCGGTCGCCTCGTCCGCCGCCGACTGGTG[T/C]
TTCCGCCTGCATGGCTGGCCTATTATGCCGCCGTTGTTGGGCGTCTACATCCTCACCGACCGGCTGCCTCGTCCGCCGCCGACTAGTTAATGAAGACATT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.50% | 22.20% | 7.91% | 5.35% | NA |
| All Indica | 2759 | 54.50% | 32.90% | 12.25% | 0.36% | NA |
| All Japonica | 1512 | 92.80% | 6.30% | 0.73% | 0.13% | NA |
| Aus | 269 | 16.70% | 14.50% | 2.60% | 66.17% | NA |
| Indica I | 595 | 77.60% | 11.10% | 11.09% | 0.17% | NA |
| Indica II | 465 | 74.00% | 17.20% | 8.82% | 0.00% | NA |
| Indica III | 913 | 24.80% | 58.90% | 15.99% | 0.33% | NA |
| Indica Intermediate | 786 | 59.90% | 28.50% | 10.81% | 0.76% | NA |
| Temperate Japonica | 767 | 98.00% | 1.70% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 83.50% | 14.70% | 1.59% | 0.20% | NA |
| Japonica Intermediate | 241 | 95.40% | 3.70% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 33.30% | 2.10% | 7.29% | 57.29% | NA |
| Intermediate | 90 | 72.20% | 6.70% | 12.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0615088191 | A -> G | LOC_Os06g25830.1 | missense_variant ; p.Val160Ala; MODERATE | nonsynonymous_codon ; V160A | Average:35.94; most accessible tissue: Minghui63 panicle, score: 59.629 | benign  |
0.16 |
TOLERATED | 0.18 |
| vg0615088191 | A -> DEL | LOC_Os06g25830.1 | N | frameshift_variant | Average:35.94; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0615088191 | 2.34E-06 | 2.25E-06 | mr1231 | 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 |
| vg0615088191 | NA | 9.26E-06 | mr1283 | 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 |
| vg0615088191 | 1.77E-06 | 7.46E-07 | mr1881 | 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 |