Supplemental Material for Mogro, Ambrosis, and Lozano, 2021

Supplementary TablesTable S1. Genomes used for ISCompare evaluationTable S2. SurroundingLen parameter optimization. Sheet 1, results of the comparison of E. coli K-12 substr. MG1655 with an artificial genome of the same strain containing 100 IS30 random insertions. Sheet 2, results of the comparison using E. meliloti strain 1021 as reference genome and an artificial E. meliloti 2011 genome with 100 ISRm5 random insertions as query. Sheet 3, Sensitivity and precision analysis. TP, true positives; FP, false positives; FN, false negatives. * indicate values manually found by inspecting the VD reports.Table S3. ISCompare evaluation using 3,000 random IS30 insertions. Sheet 1: Statistical analysis. Sheet 2: Location of 3,000 randomly inserted IS30. Set 1. Sheet 3: ISCompare results using a compilation of ISs from ISFinder database and the randomly inserted IS30 set 1. Sheet 4: Location of 3,000 randomly inserted IS30. Set 2. Sheet 5: ISCompare results using IS30 as query IS and the randomly inserted IS30 set 2. TP, true positives; FP, false positives; FN, false negatives. * indicate values manually found by inspecting the VD reports.Table S4. Analysis of differentially located ISs on P. aeruginosa strains. Sheet 1: ISCompare result analysis. TP, true positives; FP, false positives; FN, false negatives. * indicate values manually found by inspecting the VD reports. TP-ALL and FP-ALL indicate the total number of TP or FP detected. Sheet 2: ANIb and DDH results.Table S5. Analysis of differentially located ISs on E. meliloti strains. Sheet 1: ISCompare results summary. TP, true positives; FP, false positives; FN, false negatives. * indicate values manually found by inspecting the VD reports. TP-ALL and FP-ALL indicate the total number of TP or FP detected. Sheet 2: ANIb calculated using ANI matrix calculator server. Sheet 3: dDDH results from http://ggdc.dsmz.de/ggdc.php.Table S6. Comparison of ISCompare results using the normal vs the Shift mode (-S). A comparison of DLIS in E. meliloti 1021 and GR4 strains was done using ISCompare with -S option set to 5,000 nucleotides. Green shading indicates new DLIS found in the -S mode. Red shading indicates TP DLIS that were incorrectly detected by the -S mode.Table S7. Comparison of ISCompare and ISSeeker using E. meliloti genomes. E. meliloti 1021 was used as reference, and compared to GR4 and U1022 strains as queries. In the case of GR4 strain, the -S option was also evaluated. As ISSeeker only can analyse one IS at a ti