Search for Variation information by Variation ID:
Detailed information for vg0127888161:
| Variant ID: vg0127888161 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 27888161 |
| Reference Allele: CCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT | Alternative Allele: TCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT,C,GCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT |
| Primary Allele: CCCATTGGTGTTCGAGAGAT GATTCTACTCGCTCGCTGAT TCTCGAACCAGTACGTAGCA ATCTCCCGCACCGCAACCT | Secondary Allele: TCCATTGGTGTTCGAGAGAT GATTCTACTCGCTCGCTGAT TCTCGAACCAGTACGTAGCA ATCTCCCGCACCGCAACCT |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCAATCTCCCACACCATAACCTCCATTGGTGTCCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCACACCACAACC[CCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT/TCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT,C,GCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT]
CCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCAAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTGCGAGAGATGAT
Reverse complement sequence
ATCATCTCTCGCACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTTGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGG[AGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAATCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGG/AGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAATCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGA,G,AGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAATCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGC]
GGTTGTGGTGTGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGGACACCAATGGAGGTTATGGTGTGGGAGATTGCT
Allele Frequencies:
| Populations | Population Size | Frequency of CCCATTGGTGTTCGAGAGAT GATTCTACTCGCTCGCTGAT TCTCGAACCAGTACGTAGCA ATCTCCCGCACCGCAACCT(primary allele) | Frequency of TCCATTGGTGTTCGAGAGAT GATTCTACTCGCTCGCTGAT TCTCGAACCAGTACGTAGCA ATCTCCCGCACCGCAACCT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.80% | 0.30% | 1.84% | 0.80% | GCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT: 0.19%; C: 0.08% |
| All Indica | 2759 | 96.70% | 0.30% | 2.72% | 0.04% | GCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT: 0.22%; C: 0.07% |
| All Japonica | 1512 | 96.30% | 0.20% | 0.73% | 2.45% | GCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT: 0.20%; C: 0.13% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.00% | 0.22% | NA |
| Indica III | 913 | 91.20% | 0.70% | 7.34% | 0.00% | GCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT: 0.55%; C: 0.22% |
| Indica Intermediate | 786 | 98.90% | 0.10% | 0.89% | 0.00% | GCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT: 0.13% |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 89.70% | 0.60% | 1.98% | 7.14% | GCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT: 0.60% |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.41% | 0.41% | C: 0.83% |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0127888161 | CCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT -> GCCATTGGTGTTCGAGAGATGATTCTACTC GCTCGCTGATTCTCGAACCAGTACGTAGCA ATCTCCCGCACCGCAACCT | LOC_Os01g48650.1 | missense_variant ; p.Gly448Ala; MODERATE | nonsynonymous_codon ; G448A | Average:21.215; most accessible tissue: Minghui63 young leaf, score: 27.355 | benign  |
+1.365 |
N | N |
| vg0127888161 | CCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT -> TCCATTGGTGTTCGAGAGATGATTCTACTC GCTCGCTGATTCTCGAACCAGTACGTAGCA ATCTCCCGCACCGCAACCT | LOC_Os01g48650.1 | missense_variant ; p.Gly448Glu; MODERATE | nonsynonymous_codon ; G448E | Average:21.215; most accessible tissue: Minghui63 young leaf, score: 27.355 | benign |
+0.494 |
N | N |
| vg0127888161 | CCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT -> C | LOC_Os01g48650.1 | disruptive_inframe_deletion ; p.Glu422_Met447del; MODERATE | inframe_variant | Average:21.215; most accessible tissue: Minghui63 young leaf, score: 27.355 | N | N | N | N |
| vg0127888161 | CCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGATTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCT -> DEL | LOC_Os01g48650.1 | N | frameshift_variant | Average:21.215; most accessible tissue: Minghui63 young leaf, score: 27.355 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0127888161 | 1.98E-06 | NA | mr1584_2 | 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 |