Search for Variation information by Variation ID:
Detailed information for vg0805934301:
| Variant ID: vg0805934301 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 5934301 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTCTTCAGGGGTATGTCTGCACCTGTCAAGGAGGCCATCAAGCTATCGGACTATGAGCGAACGCTGAAGAAAGCATCTTCTGGAAAGTCCAAACCAGTC[T/C]
CTCAGCTTGGAGAGCAACCAAACCAGGAGATCGAGCCGTTGGTGACCGGGAAAGACATGACGATAGAAGAATTTATTATTGACACCGGTCTAACTACGGA
Reverse complement sequence
TCCGTAGTTAGACCGGTGTCAATAATAAATTCTTCTATCGTCATGTCTTTCCCGGTCACCAACGGCTCGATCTCCTGGTTTGGTTGCTCTCCAAGCTGAG[A/G]
GACTGGTTTGGACTTTCCAGAAGATGCTTTCTTCAGCGTTCGCTCATAGTCCGATAGCTTGATGGCCTCCTTGACAGGTGCAGACATACCCCTGAAGAAG
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 | 32.50% | 1.50% | 40.96% | 24.97% | NA |
| All Indica | 2759 | 5.20% | 0.10% | 56.18% | 38.53% | NA |
| All Japonica | 1512 | 88.20% | 4.50% | 5.56% | 1.72% | NA |
| Aus | 269 | 5.20% | 0.00% | 78.81% | 15.99% | NA |
| Indica I | 595 | 4.70% | 0.00% | 43.36% | 51.93% | NA |
| Indica II | 465 | 6.00% | 0.20% | 58.49% | 35.27% | NA |
| Indica III | 913 | 6.00% | 0.00% | 65.61% | 28.37% | NA |
| Indica Intermediate | 786 | 4.20% | 0.10% | 53.56% | 42.11% | NA |
| Temperate Japonica | 767 | 95.60% | 0.90% | 2.48% | 1.04% | NA |
| Tropical Japonica | 504 | 81.20% | 10.30% | 6.75% | 1.79% | NA |
| Japonica Intermediate | 241 | 79.70% | 3.70% | 12.86% | 3.73% | NA |
| VI/Aromatic | 96 | 4.20% | 1.00% | 65.62% | 29.17% | NA |
| Intermediate | 90 | 45.60% | 2.20% | 30.00% | 22.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0805934301 | T -> C | LOC_Os08g10230.1 | missense_variant ; p.Ser231Pro; MODERATE | nonsynonymous_codon ; S231P | Average:5.3; most accessible tissue: Minghui63 young leaf, score: 9.976 | possibly damaging  |
-1.664 |
TOLERATED | 1.00 |
| vg0805934301 | T -> DEL | LOC_Os08g10230.1 | N | frameshift_variant | Average:5.3; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0805934301 | NA | 9.01E-06 | mr1125 | Jap_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 |
| vg0805934301 | NA | 2.14E-06 | mr1471 | Jap_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 |
| vg0805934301 | NA | 9.42E-06 | mr1682 | Jap_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 |
| vg0805934301 | 1.42E-07 | 1.15E-08 | mr1830_2 | Jap_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 |
| vg0805934301 | NA | 8.76E-06 | mr1974_2 | Jap_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 |