Search for Variation information by Variation ID:
Detailed information for vg0334098669:
| Variant ID: vg0334098669 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34098669 |
| Reference Allele: A | Alternative Allele: C,T |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )
Flanking Sequence (100 bp) in Reference Genome:
CGGTCTCATGAACCTTTGCATGCGAGATATGCAACTCTGGAGGACTACTTGTCACCTCGTGATGGATATGCACGTCGAGCCACACAATGTCCATAGGGTT[A/C,T]
TGAAATAATTGGGCATGTATCAAGACTTCCCTCCTAGAGTTGGTCGTGCTTTGGCTGATAGTCTTCATAGGTTTGTACACATCACAGTTGTTTTATCCAA
Reverse complement sequence
TTGGATAAAACAACTGTGATGTGTACAAACCTATGAAGACTATCAGCCAAAGCACGACCAACTCTAGGAGGGAAGTCTTGATACATGCCCAATTATTTCA[T/G,A]
AACCCTATGGACATTGTGTGGCTCGACGTGCATATCCATCACGAGGTGACAAGTAGTCCTCCAGAGTTGCATATCTCGCATGCAAAGGTTCATGAGACCG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.10% | 45.20% | 0.04% | 0.61% | T: 0.02% |
| All Indica | 2759 | 82.10% | 17.00% | 0.07% | 0.91% | NA |
| All Japonica | 1512 | 2.10% | 97.80% | 0.00% | 0.07% | NA |
| Aus | 269 | 79.90% | 20.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.70% | 12.80% | 0.00% | 0.50% | NA |
| Indica II | 465 | 93.80% | 5.40% | 0.22% | 0.65% | NA |
| Indica III | 913 | 71.40% | 27.80% | 0.00% | 0.77% | NA |
| Indica Intermediate | 786 | 84.00% | 14.40% | 0.13% | 1.53% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 5.20% | 94.60% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 5.20% | 93.80% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 44.40% | 52.20% | 0.00% | 2.22% | T: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334098669 | A -> C | LOC_Os03g59910.1 | missense_variant ; p.Met100Leu; MODERATE | nonsynonymous_codon ; M100L | Average:44.668; most accessible tissue: Zhenshan97 young leaf, score: 54.618 | possibly damaging  |
-1.797 |
TOLERATED | 1.00 |
| vg0334098669 | A -> DEL | LOC_Os03g59910.1 | N | frameshift_variant | Average:44.668; most accessible tissue: Zhenshan97 young leaf, score: 54.618 | N | N | N | N |
| vg0334098669 | A -> T | LOC_Os03g59910.1 | missense_variant ; p.Met100Leu; MODERATE | nonsynonymous_codon ; M100L | Average:44.668; most accessible tissue: Zhenshan97 young leaf, score: 54.618 | possibly damaging |
-1.797 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0334098669 | NA | 3.28E-06 | mr1098 | 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 |
| vg0334098669 | NA | 2.10E-10 | mr1249 | 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 |
| vg0334098669 | NA | 9.72E-06 | mr1305 | 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 |
| vg0334098669 | NA | 7.12E-06 | mr1961 | 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 |
| vg0334098669 | NA | 2.16E-09 | mr1198_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 |
| vg0334098669 | NA | 2.90E-14 | mr1579_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 |