Table 1 Nine repeat loci with the repeat count detection by Sanger sequencing, HipSTR on 300X short-read data and DeepRepeat/Tandem-genotypes/RepeatHMM on 38X long read data for NA12878
From: DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing
Repeat loci | Motif | GRCh38 length | Sanger | HipSTR | DeepRepeat | Tandem-genotypes | RepeatHMM | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
chr12:4702128-4702202 | CCA | 74 | 23 | 24 | 25 | 25 | 27 | 27 | 26 | 27 | 24 | 24 |
chr17:10995712-10995775 | CTG | 63 | 19 | 20 | 20 | 20 | 20 | 20 | 20 | 22 | 19 | 20 |
chr16:73546662-73546741 | TGC | 79 | 25 | 26 | 24 | 24 | 27 | 27 | 24 | 24 | 21 | 23 |
chr7:152384548-152384614 | CAC | 66 | 19 | 22 | 18 | 20 | 20 | 24 | 22 | 25 | 20 | 23 |
chr1:161051967-161052060 | CAC | 93 | 21 | 26 | N.A. | N.A. | 19 | 24 | 21 | 26 | 21 | 26 |
chrX:55366379-55366473 | TATC | 94 | 22 | 23 | 23 | 23 | 24 | 24 | 23 | 23 | 23 | 24 |
chr10:107609688-107609784 | ATCT | 96 | 18 | 21 | 19 | 22 | 19 | 22 | 19 | 23 | 19 | 22 |
chr6:145272942-145273029 | AGAT | 87 | 14 | 18 | 14 | 18 | 14 | 18 | 14 | 17 | 14 | 19 |
chr4:42555085-42555198 | TATC | 113 | 26 | 27 | 26 | 27 | 28 | 28 | 27 | 28 | 27 | 27 |