Search for Variation information by Variation ID:
Detailed information for vg0143001519:
| Variant ID: vg0143001519 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001519 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATCTGTAGGTAGGCGTAGTGGACCGCCGCCATGAACTTCACCAACGCGGGCCTCCCCAGGACCGCGTTGTAGGGCAGACTGAGGTCCGCCACATCGAAGT[T/C]
CACCCGCTCCATGCGGAAGTTGGCGGATCCACCGAAGGTGACCGGTAGGTCGATGTGACCTAACGGCCACGTGTGCCCCGGCGTCACACCGATAATTGGC
Reverse complement sequence
GCCAATTATCGGTGTGACGCCGGGGCACACGTGGCCGTTAGGTCACATCGACCTACCGGTCACCTTCGGTGGATCCGCCAACTTCCGCATGGAGCGGGTG[A/G]
ACTTCGATGTGGCGGACCTCAGTCTGCCCTACAACGCGGTCCTGGGGAGGCCCGCGTTGGTGAAGTTCATGGCGGCGGTCCACTACGCCTACCTACAGAT
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 | 7.70% | 2.50% | 3.91% | 85.93% | NA |
| All Indica | 2759 | 1.20% | 0.70% | 3.04% | 95.07% | NA |
| All Japonica | 1512 | 20.70% | 0.00% | 2.05% | 77.25% | NA |
| Aus | 269 | 1.10% | 35.70% | 23.42% | 39.78% | NA |
| Indica I | 595 | 1.70% | 0.00% | 0.67% | 97.65% | NA |
| Indica II | 465 | 1.70% | 0.40% | 2.15% | 95.70% | NA |
| Indica III | 913 | 0.50% | 0.50% | 3.29% | 95.62% | NA |
| Indica Intermediate | 786 | 1.40% | 1.40% | 5.09% | 92.11% | NA |
| Temperate Japonica | 767 | 37.70% | 0.00% | 1.30% | 61.02% | NA |
| Tropical Japonica | 504 | 1.80% | 0.00% | 2.38% | 95.83% | NA |
| Japonica Intermediate | 241 | 6.20% | 0.00% | 3.73% | 90.04% | NA |
| VI/Aromatic | 96 | 0.00% | 2.10% | 3.12% | 94.79% | NA |
| Intermediate | 90 | 13.30% | 2.20% | 4.44% | 80.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001519 | T -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:17.621; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| vg0143001519 | T -> C | LOC_Os01g74230.1 | missense_variant ; p.Asn519Asp; MODERATE | nonsynonymous_codon | Average:17.621; most accessible tissue: Zhenshan97 panicle, score: 46.362 | benign  |
-0.285 |
TOLERATED | 0.11 |