Table S6.

Variants selected in parallel in each treatment, as plotted in Fig. 2

TreatmentReplicateVariant typeChromosome position (bp)Frequency (n = 40)AnnotationVirulence category
Control1Deletion19436421PA0171No virulence known
Control1SNP4368954pilT (PA0395)Type IV pilus
Control1SNP173341829braB (PA1590)No virulence known
Control1Insertion18947605cysB (PA1754)No virulence known
Control1SNP36629379PA3271No virulence known
Control1SNP37913494amrZ (PA3385)Flagellum
Control1Deletion37915851amrZ (PA3385)Flagellum
Control1Insertion401541616glpR (PA3583)No virulence known
Control1Insertion51011625pilY1 (PA4554)Type IV pilus
Control1Deletion510133115pilY1 (PA4554)Type IV pilus
Control1Deletion55589597motB (PA4953)Flagellum
Control2Deletion4371302pilT (PA0395)Type IV pilus
Control2SNP11626464braC (PA1074)No virulence known
Control2SNP11880915fleQ (PA1097)Biofilm formation
Control2SNP18943076cysB (PA1754)No virulence known
Control2SNP18945014cysB (PA1754)No virulence known
Control2SNP24497844PA2228No virulence known
Control2SNP28310007antB (PA2513)No virulence known
Control2SNP36620189PA3271No virulence known
Control2SNP36629376PA3271No virulence known
Control2Insertion40154167glpR (PA3583)No virulence known
Control2Deletion40154362glpR (PA3583)No virulence known
Control2SNP40583977rpoS (PA3622)Biofilm formation
Control2SNP44092777PA3933No virulence known
Control2Deletion48956405bifA (PA4367)Type IV pilus
Control2SNP50693423pilA (PA4525)Type IV pilus
Control2SNP50705947pilB (PA4526)Type IV pilus
Control2SNP50724257pilC (PA4527)Type IV pilus
Control2Deletion55589597motB (PA4953)Flagellum
Control2SNP57492915hutC (PA5105)No virulence known
Control3Insertion157205416PA1442Flagellum
Control3SNP16996738aer (PA1561)Flagellum
Control3SNP173312713braB (PA1590)No virulence known
Control3SNP173341810braB (PA1590)No virulence known
Control3Insertion17337017braB (PA1590)No virulence known
Control3Indels189443310cysB (PA1754)No virulence known
Control3Deletion189443812cysB (PA1754)No virulence known
Control3Deletion18949131cysB (PA1754)No virulence known
Control3SNP28310005antB (PA2513)No virulence known
Control3SNP30038697PA2654Flagellum
Control3SNP366185011PA3271No virulence known
Control3SNP379160913amrZ (PA3385)Flagellum
Control3Indels390612618PA3488No virulence known
Control3Indels401541632glpR (PA3583)No virulence known
Control3Deletion405589931mutS (PA3620)No virulence known
Control3SNP405852830rpoS (PA3622)Biofilm formation
Control3SNP41468294wspE (PA3704)No virulence known
Control3SNP44099684PA3933No virulence known
Control3SNP48608297PA4332Biofilm formation
Control3SNP50693425pilA (PA4525)Type IV pilus
Control3SNP50711354pilB (PA4526)Type IV pilus
Control3Insertion555974212motA (PA4954)Flagellum
Control3SNP589146313PA5233Flagellum
Control4Deletion4371301pilT (PA0395)Type IV pilus
Control4SNP11619065braC (PA1074)No virulence known
Control4SNP116243910braC (PA1074)No virulence known
Control4SNP169970910aer (PA1561)Flagellum
Control4SNP173276119braB (PA1590)No virulence known
Control4Deletion17337762braB (PA1590)No virulence known
Control4SNP24499177PA2228No virulence known
Control4SNP36622469PA3271No virulence known
Control4SNP37914238amrZ (PA3385)Flagellum
Control4Insertion40154166glpR (PA3583)No virulence known
Control4SNP48608298PA4332Biofilm formation
Control4Deletion50726068pilC (PA4527)Type IV pilus
Control4SNP55597578motA (PA4954)Flagellum
Control4Deletion58912448PA5233Flagellum
Control5Deletion1943641PA0171No virulence known
Control5SNP17334187braB (PA1590)No virulence known
Control5SNP18943498cysB (PA1754)No virulence known
Control5Deletion18943972cysB (PA1754)No virulence known
Control5SNP18951614cysB (PA1754)No virulence known
Control5SNP28310005antB (PA2513)No virulence known
Control5SNP366201217PA3271No virulence known
Control5SNP379147416amrZ (PA3385)Flagellum
Control5Deletion40160986glpR (PA3583)No virulence known
Control5SNP48607667PA4332Biofilm formation
Control5SNP48608087PA4332Biofilm formation
Control5Insertion48947685bifA (PA4367)Type IV pilus
Control5SNP555965017motA (PA4954)Flagellum
Control5Deletion57384465PA5097No virulence known
Control5SNP57491117hutC (PA5105)No virulence known
Control6SNP43714724pilT (PA0395)Type IV pilus
Control6SNP118894624fleQ (PA1097)Biofilm formation
Control6Insertion15723733PA1442Flagellum
Control6SNP169881023aer (PA1561)Flagellum
Control6SNP173284913braB (PA1590)No virulence known
Control6SNP189427018cysB (PA1754)No virulence known
Control6SNP300448716PA2654Flagellum
Control6SNP366171726PA3271No virulence known
Control6Deletion379140025amrZ (PA3385)Flagellum
Control6Deletion390612621PA3488No virulence known
Control6Insertion40154169glpR (PA3583)No virulence known
Control6Insertion40552762mutS (PA3620)No virulence known
Control6SNP405565424mutS (PA3620)No virulence known
Control6SNP414767014wspE (PA3704)No virulence known
Control6SNP50693424pilA (PA4525)Type IV pilus
Control6SNP51033788pilY1 (PA4554)Type IV pilus
Control6SNP55583583motB (PA4953)Flagellum
Control6Insertion555982224motA (PA4954)Flagellum
Control6Deletion57384543PA5097No virulence known
Control6Deletion57491118hutC (PA5105)No virulence known
Control6SNP589120423PA5233Flagellum
Phages1SNP96978720acsA (PA0887)No virulence known
Phages1Prophage integration108629018mvfR (PA1003)Quorum sensing
Phages1Prophage integration10866489mvfR (PA1003)Quorum sensing
Phages1Prophage integration10869754mvfR (PA1003)Quorum sensing
Phages1SNP11618765braC (PA1074)No virulence known
Phages1SNP11628515braC (PA1074)No virulence known
Phages1Prophage integration155871738lasR (PA1430)Quorum sensing
Phages1SNP17327173braB (PA1590)No virulence known
Phages1SNP17334189braB (PA1590)No virulence known
Phages1SNP18943994cysB (PA1754)No virulence known
Phages1SNP189463019cysB (PA1754)No virulence known
Phages1SNP366229020PA3271No virulence known
Phages1Insertion379137210amrZ (PA3385)Flagellum
Phages1Deletion40154166glpR (PA3583)No virulence known
Phages1SNP40155174glpR (PA3583)No virulence known
Phages1Deletion55589591motB (PA4953)Flagellum
Phages1SNP555932917motA (PA4954)Flagellum
Phages1Deletion57487791hutC (PA5105)No virulence known
Phages2SNP97128513acsA (PA0887)No virulence known
Phages2Prophage integration108642215mvfR (PA1003)Quorum sensing
Phages2Prophage integration10869753mvfR (PA1003)Quorum sensing
Phages2Prophage integration155871734lasR (PA1430)Quorum sensing
Phages2Prophage integration15588344lasR (PA1430)Quorum sensing
Phages2Deletion16993472aer (PA1561)Flagellum
Phages2SNP17334109braB (PA1590)No virulence known
Phages2SNP17334199braB (PA1590)No virulence known
Phages2SNP189428912cysB (PA1754)No virulence known
Phages2Deletion18946653cysB (PA1754)No virulence known
Phages2SNP28310006antB (PA2513)No virulence known
Phages2SNP28608123PA2533No virulence known
Phages2SNP366195414PA3271No virulence known
Phages2Indels401541614glpR (PA3583)No virulence known
Phages2SNP40154294glpR (PA3583)No virulence known
Phages2Prophage integration489558719bifA (PA4367)Type IV pilus
Phages2SNP555965013motA (PA4954)Flagellum
Phages3Deletion9890140fha1 (PA0081)T6SS
Phages3Deletion97136521acsA (PA0887)No virulence known
Phages3Prophage integration10869751mvfR (PA1003)Quorum sensing
Phages3SNP116220312braC (PA1074)No virulence known
Phages3Deletion173314111braB (PA1590)No virulence known
Phages3SNP189437022cysB (PA1754)No virulence known
Phages3SNP366320421PA3271No virulence known
Phages3Insertion379142524amrZ (PA3385)Flagellum
Phages3Indels401541614glpR (PA3583)No virulence known
Phages3Prophage integration510365635pilY1 (PA4554)Type IV pilus
Phages4Deletion9890138fha1 (PA0081)T6SS
Phages4SNP9711568acsA (PA0887)No virulence known
Phages4Prophage integration108700724mvfR (PA1003)Quorum sensing
Phages4SNP158455011fleN (PA1454)Biofilm formation
Phages4SNP169875915aer (PA1561)Flagellum
Phages4SNP17334097braB (PA1590)No virulence known
Phages4SNP189469615cysB (PA1754)No virulence known
Phages4SNP28614484PA2533No virulence known
Phages4SNP366194911PA3271No virulence known
Phages4SNP379140811amrZ (PA3385)Flagellum
Phages4SNP555888012motB (PA4953)Flagellum
Phages4SNP555982416motA (PA4954)Flagellum
Phages4SNP56410498PA5017No virulence known
Phages5Deletion9890137fha1 (PA0081)T6SS
Phages5SNP11622965braC (PA1074)No virulence known
Phages5Prophage integration155844536lasR (PA1430)Quorum sensing
Phages5SNP158416111fleN (PA1454)Biofilm formation
Phages5Deletion16998749aer (PA1561)Flagellum
Phages5SNP173341837braB (PA1590)No virulence known
Phages5Insertion18944338cysB (PA1754)No virulence known
Phages5SNP18944694cysB (PA1754)No virulence known
Phages5SNP28310008antB (PA2513)No virulence known
Phages5SNP366286111PA3271No virulence known
Phages5Insertion401541628glpR (PA3583)No virulence known
Phages5SNP405540737mutS (PA3620)No virulence known
Phages5Prophage integration48949915bifA (PA4367)Type IV pilus
Phages5SNP49471289ftsW (PA4413)No virulence known
Phages5SNP555888711motB (PA4953)Flagellum
Phages5SNP555918211motA (PA4954)Flagellum
Phages5SNP564232111PA5017No virulence known
Phages6Prophage integration155850819lasR (PA1430)Quorum sensing
Phages6SNP169878012aer (PA1561)Flagellum
Phages6SNP173276114braB (PA1590)No virulence known
Phages6SNP17327744braB (PA1590)No virulence known
Phages6SNP17334184braB (PA1590)No virulence known
Phages6SNP17336493braB (PA1590)No virulence known
Phages6SNP189437112cysB (PA1754)No virulence known
Phages6SNP366243814PA3271No virulence known
Phages6Deletion40160987glpR (PA3583)No virulence known
Phages6SNP40548585mutS (PA3620)No virulence known
Phages6SNP49471284ftsW (PA4413)No virulence known
Phages6SNP57491053hutC (PA5105)No virulence known