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Table 1 Average number of correctly detected simulated differences by NucDiff with different parameter settings and QUAST

From: NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences

Difference Truth Default c30 c120 l10 l65 b80 b350 QUAST-like QUAST
insertion 1650 1634 1634 1634 1634 1634 1632 1634 1634 858
deletion 1719 1678 1678 1678 1677 1678 1679 1676 1674 465
duplication 251 136 122 150 136 136 137 124 136 196
tandem_duplication 60 57 57 57 57 57 60 54 57 57
collapsed_repeat 58 53 53 53 53 53 54 51 53 53
collapsed_tandem_repeat 59 55 55 55 55 55 56 53 55 55
relocation 217 127 142 108 127 127 136 112 127 130
relocation-insertion 13 13 13 13 13 13 13 13 13 13
relocation-insertion_ATGC 13 13 13 13 13 13 13 13 13 13
relocation-inserted_gap 13 13 13 13 13 13 13 13 13 13
relocation-overlap 13 13 13 13 13 13 13 13 13 12
translocation 111 50 57 43 50 50 50 50 50 62
translocation-insertion 13 12 12 12 12 12 12 12 12 13
translocation-insertion_ATGC 13 13 13 13 13 13 13 13 13 13
translocation-inserted_gap 13 13 13 13 13 13 13 13 13 13
translocation-overlap 13 13 13 13 13 13 13 13 13 11
inversion 534 530 530 528 529 530 531 526 530 528
reshuffling 2585 2585 2585 2585 2585 2585 2585 2585 2585 2536
substitution 115 81 81 81 80 81 89 68 81 84
gap 49 46 46 46 46 46 48 46 45 34
inserted_gap 21 21 21 21 21 21 21 21 20 16
mapped_seq 13 10 11 6 10 10 10 10 10 10
unaligned_sequence 13 13 13 13 13 13 13 13 13 13