Table 3 Novel variants in HG002 genome, missing in v3.3.2 benchmark variant, discovered by Sanger sequencing together with the prediction information by NanoCaller and other variant callers using ONT reads basecall with Guppy 2.3.4. NanoCaller model used was trained on ONT HG001 Guppy 2.3.8 basecalled reads
Chrom | Position | REF | ALT | Genotype | Nanocaller | Medaka | Clair | Longshot |
|---|---|---|---|---|---|---|---|---|
chr1 | 78883942 | C | T | 1|0 | Correct | – | – | – |
chr1 | 78883952 | ATATATATTTATCCTTTATATATATATTCTT | A | 1|0 | – | – | – | – |
chr2 | 227913871 | A | ATATCTATCTATC | 1|0 | Correct | Correct | Correct | – |
chr2 | 227913885 | G | A | 1|0 | Correct | Correct | Correct | Correct |
chr2 | 227913889 | G | A | 1|0 | Correct | Correct | Correct | Correct |
chr2 | 227913928 | T | TA | 1|0 | Wrong allele | Correct | – | – |
chr2 | 227913931 | A | T | 1|0 | Correct | – | – | – |
chr3 | 5336450 | A | T,C | 1|2 | Correct | Wrong allele | Wrong allele | Wrong allele |
chr3 | 5336452 | C | CGCGT | 0|1 | – | – | – | – |
chr3 | 5336465 | ACACACACACACG | A | 0|1 | Wrong variant type | Wrong allele | – | – |
chr3 | 5336477 | GCA | G | 1|0 | Wrong allele | Correct | Wrong allele | – |
chr3 | 5336487 | A | G | 0|1 | Wrong variant type | Wrong variant type | – | – |
chr6 | 160009985 | C | CTTAA | 0|1 | Wrong allele | – | Wrong allele | – |
chr6 | 160009986 | C | A | 0|1 | Wrong zygosity | Wrong allele | Wrong variant type | Wrong allele and zygosity |
chr6 | 167130970 | G | GGGCCCCCCTCCCTCCGGGACTCCTCCCTCT | 0|1 | – | – | – | – |
chr6 | 167130972 | GA | G | 1|0 | – | Wrong zygosity | Wrong zygosity | – |
chr6 | 167130973 | A | G | 0|1 | – | – | – | – |
chr6 | 167130976 | A | C | 1|1 | Correct | Wrong zygosity | Correct | Correct |
chr6 | 167130986 | T | C | 1|0 | Correct | Wrong allele | – | Wrong allele |
chr6 | 167130989 | A | G | 1|1 | Correct | Correct | Correct | Correct |
chr6 | 167130990 | C | A | 1|0 | – | – | – | – |
chr6 | 167130992 | C | T | 1|0 | Correct | – | Correct | Correct |
chr9 | 134784949 | C | T | 0|1 | Correct | Correct | Correct | Correct |
chr9 | 134784951 | G | T | 0|1 | – | – | – | – |
chr9 | 134784955 | G | GGGGGGCA | 0|1 | – | – | – | – |
chr9 | 134784956 | T | G | 0|1 | Correct | Wrong variant type | Wrong variant type | – |
chr9 | 135663795 | ACAGAGGGGGACCTGGAGGGGCAGAGGAGAGACCTGTGGGG | A | 0|1 | – | – | – | – |
chr9 | 135663892 | A | G | 1|1 | Wrong zygosity | Correct | Correct | Correct |
chr9 | 135663893 | T | A,G | 1|2 | Correct | Wrong allele | Wrong allele | Wrong allele |
chr11 | 113466435 | G | GC | 1|1 | – | Correct | Correct | – |
chr11 | 113466437 | A | T | 1|1 | Correct | Wrong allele | Wrong allele | Wrong allele |
chr12 | 100940063 | A | AT | 0|1 | Correct | – | – | – |
chr12 | 100940065 | G | C | 0|1 | Correct | Wrong allele | – | – |
chr14 | 75318035 | C | T | 1|0 | Correct | Correct | Correct | Correct |
chr14 | 75318038 | AT | A | 1|0 | – | Wrong allele | Correct | – |
chr14 | 75318052 | T | C | 1|0 | Correct | – | – | – |
chr14 | 75318054 | T | G | 1|0 | – | – | – | – |
chr20 | 11064571 | T | TGA | 0|1 | – | Wrong allele | – | – |
chr20 | 11064574 | A | ATTTTCAAGACTATTGTGACTATGAC | 0|1 | – | Correct | – | – |
chr20 | 11064578 | A | T | 0|1 | Correct | – | – | – |
chr20 | 11064579 | C | T | 0|1 | Correct | Correct | Wrong variant type | – |