Search for Variation information by Variation ID:
Detailed information for vg0403068602:
| Variant ID: vg0403068602 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 3068602 |
| Reference Allele: A | Alternative Allele: G,AAAGATG |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 81. )
Flanking Sequence (100 bp) in Reference Genome:
AACTCCACTGTTCTGGTTCGTACTCTTTTTGTCTTGGGCTCTCGTGTAAAAAGTGTATCCATTGATTTCATAACCTTGGAATGTAGTTATGGAGCCGGAG[A/G,AAAGATG]
GTCCCCTAGCCAAGAAGGCTAGTTGTCGGTCAATTGTCTCGTTACCCAGGAGGTGTTCTCGCTGCCAAGCGGGGAAAGTATCAATATGATGGCGTGTAAT
Reverse complement sequence
ATTACACGCCATCATATTGATACTTTCCCCGCTTGGCAGCGAGAACACCTCCTGGGTAACGAGACAATTGACCGACAACTAGCCTTCTTGGCTAGGGGAC[T/C,CATCTTT]
CTCCGGCTCCATAACTACATTCCAAGGTTATGAAATCAATGGATACACTTTTTACACGAGAGCCCAAGACAAAAAGAGTACGAACCAGAACAGTGGAGTT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.10% | 15.20% | 17.52% | 13.14% | AAAGATG: 0.04% |
| All Indica | 2759 | 75.20% | 4.30% | 17.91% | 2.50% | AAAGATG: 0.04% |
| All Japonica | 1512 | 15.30% | 37.60% | 15.41% | 31.61% | AAAGATG: 0.07% |
| Aus | 269 | 69.50% | 5.90% | 14.50% | 10.04% | NA |
| Indica I | 595 | 94.50% | 3.20% | 2.02% | 0.34% | NA |
| Indica II | 465 | 67.10% | 7.30% | 23.23% | 2.37% | NA |
| Indica III | 913 | 69.40% | 1.00% | 25.96% | 3.50% | AAAGATG: 0.11% |
| Indica Intermediate | 786 | 72.30% | 7.30% | 17.43% | 3.05% | NA |
| Temperate Japonica | 767 | 11.50% | 61.30% | 13.30% | 13.95% | NA |
| Tropical Japonica | 504 | 14.90% | 10.90% | 17.26% | 56.94% | NA |
| Japonica Intermediate | 241 | 28.20% | 18.30% | 18.26% | 34.85% | AAAGATG: 0.41% |
| VI/Aromatic | 96 | 14.60% | 1.00% | 40.62% | 43.75% | NA |
| Intermediate | 90 | 55.60% | 13.30% | 25.56% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403068602 | A -> DEL | LOC_Os04g05930.1 | N | frameshift_variant | Average:27.661; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
| vg0403068602 | A -> AAAGATG | LOC_Os04g05930.1 | inframe_insertion ; p.Leu342delinsProSerPhe; MODERATE | inframe_variant | Average:27.661; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
| vg0403068602 | A -> G | LOC_Os04g05930.1 | missense_variant ; p.Leu342Pro; MODERATE | nonsynonymous_codon ; L342P | Average:27.661; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | possibly damaging  |
-1.728 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403068602 | NA | 5.14E-06 | mr1069 | 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 |
| vg0403068602 | NA | 6.46E-07 | mr1164 | 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 |
| vg0403068602 | NA | 2.52E-06 | mr1183 | 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 |
| vg0403068602 | NA | 2.11E-06 | mr1229 | 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 |
| vg0403068602 | NA | 4.62E-06 | mr1503 | 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 |
| vg0403068602 | NA | 2.49E-07 | mr1880 | 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 |
| vg0403068602 | 3.80E-06 | 1.42E-07 | mr1955 | 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 |