chrom first_breakpoint_start first_breakpoint_end second_breakpoint_start second_breakpoint_end start_gene_id end_gene_id breakpoint_name breakpoint_id target_gene use note Pf3D7_05_v3 938329 938357 980012 980040 PF3D7_0522900 PF3D7_0523000 42kb around MDR1 PfMDR1_dup_1 MDR1 1 Pf3D7_05_v3 949514 949527 967253 967266 PF3D7_0522900 PF3D7_0523000 17.7kb around MDR1 PfMDR1_dup_2 MDR1 1 Pf3D7_05_v3 947790 947800 962444 962454 PF3D7_0522900 PF3D7_0523000 15kb around MDR1 PfMDR1_dup_3 MDR1 1 Corresponds to PfMDR1_Nair_8 Pf3D7_05_v3 953961 953982 973008 973034 PF3D7_0523000 PF3D7_0523100 19kb around MDR1 PfMDR1_dup_4 MDR1 1 Corresponds to PfMDR1_Nair_13. Similar to PfMDR1_Nair_12 but fewer calls Pf3D7_05_v3 953961 953982 965409 865428 PF3D7_0523000 PF3D7_0523100 11kb around MDR1 PfMDR1_dup_5 MDR1 1 Pf3D7_05_v3 947968 947986 969783 969812 PF3D7_0523000 PF3D7_0523200 22kb around MDR1 PfMDR1_dup_6 MDR1 1 Pf3D7_05_v3 953961 953982 970215 970252 PF3D7_0523000 PF3D7_0523100 16kb around MDR1 PfMDR1_dup_7 MDR1 1 Corresponds to PfMDR1_Nair_4/PfMDR1_Nair_7 Pf3D7_05_v3 780906 780927 980012 980040 PF3D7_0518800 PF3D7_0523600 199kb around MDR1 PfMDR1_dup_8 MDR1 1 Pf3D7_05_v3 870473 870502 964628 964646 PF3D7_0521300 PF3D7_0523100 94kb around MDR1 PfMDR1_dup_9 MDR1 1 Pf3D7_05_v3 795494 795527 964505 964540 PF3D7_0519300 PF3D7_0519300 169kb around MDR1 PfMDR1_dup_10 MDR1 1 Pf3D7_05_v3 888324 888349 970215 970252 PF3D7_0521900 PF3D7_0523200 82kb around MDR1 PfMDR1_dup_11 MDR1 1 Corresponds to PfMDR1_Nair_DD2 Pf3D7_05_v3 868667 868699 964505 964540 PF3D7_0521200 PF3D7_0523100 96kb around MDR1 PfMDR1_dup_12 MDR1 1 Corresponds to PfMDR1_Nair_B8 Pf3D7_05_v3 946696 946717 964505 964540 PF3D7_0522900 PF3D7_0523100 18kb around MDR1 PfMDR1_dup_13 MDR1 1 Pf3D7_05_v3 946696 946717 970215 970252 PF3D7_0522900 PF3D7_0523100 24kb around MDR1 PfMDR1_dup_14 MDR1 1 Similar to both PfMDR1_Nair_3 and PfMDR1_Nair_9, though has fewer faceaway pairs Pf3D7_05_v3 946346 946375 970215 970252 PfMDR1_dup_15 PfMDR1_dup_15 MDR1 1 Similar to PfMDR1_Nair_3 Pf3D7_05_v3 948197 948217 976430 976456 PfMDR1_dup_16 PfMDR1_dup_16 MDR1 1 Similar to PfMDR1_Nair_2 Pf3D7_05_v3 946346 946375 986036 986067 PfMDR1_dup_17 PfMDR1_dup_17 MDR1 1 Similar to PfMDR1_Nair_1 Pf3D7_05_v3 953961 953982 976144 976170 PfMDR1_dup_18 PfMDR1_dup_18 MDR1 1 Pf3D7_05_v3 953961 953982 989700 989721 PfMDR1_dup_19 PfMDR1_dup_19 MDR1 1 Similar to PfMDR1_Nair_5 Pf3D7_05_v3 946696 946717 969783 969812 PfMDR1_dup_20 PfMDR1_dup_20 MDR1 1 Similar to PfMDR1_Nair_9 Pf3D7_05_v3 946346 946375 973140 973162 PfMDR1_dup_21 PfMDR1_dup_21 MDR1 1 Pf3D7_05_v3 943418 943437 970215 970252 PfMDR1_dup_22 PfMDR1_dup_22 MDR1 1 Pf3D7_05_v3 942351 942376 970215 970252 PfMDR1_dup_23 PfMDR1_dup_23 MDR1 1 Pf3D7_05_v3 939060 939083 976144 976170 PfMDR1_dup_24 PfMDR1_dup_24 MDR1 1 Pf3D7_05_v3 938329 938357 973140 973162 PfMDR1_dup_25 PfMDR1_dup_25 MDR1 1 Pf3D7_05_v3 953961 953982 976430 976456 PfMDR1_dup_26 PfMDR1_dup_26 MDR1 1 Pf3D7_05_v3 937002 937024 969783 969812 PfMDR1_dup_27 PfMDR1_dup_27 MDR1 1 Pf3D7_05_v3 946346 946375 978174 978199 PfMDR1_dup_28 PfMDR1_dup_28 MDR1 1 Pf3D7_05_v3 946617 946617 986030 986030 PF3D7_0522900 PF3D7_0523700 Nair 1 MDR1 PfMDR1_Nair_1 MDR1 0 Similar to PfMDR1_dup_17 Pf3D7_05_v3 948204 948204 976440 976440 PF3D7_0522900 PF3D7_0523400 Nair 2 MDR1 PfMDR1_Nair_2 MDR1 0 Similar to PfMDR1_dup_16 Pf3D7_05_v3 946351 946351 970240 970240 Nair 3 MDR1 PfMDR1_Nair_3 MDR1 0 Similar to PfMDR1_dup_14, though has fewer faceaway pairs. Also similar but distinct from PfMDR1_Nair_9 Pf3D7_05_v3 953950 953950 970240 970240 Nair 4 MDR1 PfMDR1_Nair_4 MDR1 0 Corresponds to PfMDR1_dup_7, identical to PfMDR1_Nair_7 Pf3D7_05_v3 953950 953950 989750 989750 Nair 5 MDR1 PfMDR1_Nair_5 MDR1 0 Corresponds to PfMDR1_dup_19 Pf3D7_05_v3 942350 942350 992081 992081 Nair 6 MDR1 PfMDR1_Nair_6 MDR1 0 Only few reads mapping, so ignored Pf3D7_05_v3 953950 953950 970240 970240 Nair 7 MDR1 PfMDR1_Nair_7 MDR1 0 Corresponds to PfMDR1_dup_7, identical to PfMDR1_Nair_4 Pf3D7_05_v3 947783 947783 962437 962437 Nair 8 MDR1 PfMDR1_Nair_8 MDR1 0 Corresponds to PfMDR1_dup_3 Pf3D7_05_v3 946690 946690 969790 969790 Nair 9 MDR1 PfMDR1_Nair_9 MDR1 0 Similar to PfMDR1_dup_14, though has fewer faceaway pairs. Also similar but distinct from PfMDR1_Nair_3 Pf3D7_05_v3 953950 953950 973150 973150 Nair 12 MDR1 PfMDR1_Nair_12 MDR1 0 Similar to PfMDR1_dup_4 and PfMDR1_Nair_13, but more calls Pf3D7_05_v3 953950 953950 973004 973004 Nair 13 MDR1 PfMDR1_Nair_13 MDR1 0 Corresponds to PfMDR1_dup_4. Similar to PfMDR1_Nair_12 but fewer calls Pf3D7_05_v3 948458 948458 974010 974010 Nair 15 MDR1 PfMDR1_Nair_15 MDR1 0 Only few reads mapping, so ignored Pf3D7_05_v3 868690 868690 964500 964500 Nair B8 MDR1 PfMDR1_Nair_B8 MDR1 0 Corresponds to PfMDR1_dup_12 Pf3D7_05_v3 888335 888335 970240 970240 Nair DD2 MDR1 PfMDR1_Nair_DD2 MDR1 0 Corresponds to PfMDR1_dup_11 Pf3D7_14_v3 283034 283069 300493 300522 PF3D7_1407800 PF3D7_1409200 17kb from plasmepsin IV PfPlasmepsin_2 plasmepsin 1 Pf3D7_14_v3 283034 283069 362990 363020 PF3D7_1407800 PF3D7_1409200 80kb from plasmepsin IV PfPlasmepsin_3 plasmepsin 1 Pf3D7_14_v3 289611 289621 298782 298792 PF3D7_1407800 PF3D7_1409200 plasmepsin I to plasmepsin III PfPlasmepsin_1 plasmepsin 1 Pf3D7_12_v3 973800 973825 974241 974276 GCH1 promoter PfGCH1_promoter_dup_1 GCH1 0 First mentioned in Ravenhall 2016. Was giving very many calls (about half of samples), so dropped until further investigation Pf3D7_12_v3 968847 968881 977926 977949 PfGCH1_dup_1 PfGCH1_dup_1 GCH1 1 Pf3D7_12_v3 946265 946284 980622 980659 PfGCH1_dup_2 PfGCH1_dup_2 GCH1 1 Pf3D7_12_v3 959516 959540 978164 978191 PfGCH1_dup_3 PfGCH1_dup_3 GCH1 1 Pf3D7_12_v3 970992 971023 975712 975747 PfGCH1_dup_4 PfGCH1_dup_4 GCH1 1 Pf3D7_12_v3 953141 953174 978164 978191 PfGCH1_dup_5 PfGCH1_dup_5 GCH1 1 Pf3D7_12_v3 959516 959540 981032 981060 PfGCH1_dup_6 PfGCH1_dup_6 GCH1 1 Pf3D7_12_v3 974100 974119 986443 986465 PfGCH1_dup_7 PfGCH1_dup_7 GCH1 1 Pf3D7_12_v3 973800 973825 976004 976045 PfGCH1_dup_8 PfGCH1_dup_8 GCH1 1 Pf3D7_12_v3 968847 968881 976155 976170 PfGCH1_dup_9 PfGCH1_dup_9 GCH1 1 Pf3D7_12_v3 945388 945416 977926 977949 PfGCH1_dup_10 PfGCH1_dup_10 GCH1 1 Pf3D7_12_v3 974251 974251 976019 976019 PF3D7_1224000 PF3D7_1224000 Nair 1.8kb GCH1 PfGCH1_Nair_1 GCH1 0 Similar to PfGCH1_Nair_2 but fewer calls. Also similar to PfGCH1_dup_8 Pf3D7_12_v3 973801 973801 976019 976019 PF3D7_1224000 PF3D7_1224000 Nair 2.2kb GCH1 PfGCH1_Nair_2 GCH1 0 Similar to PfGCH1_Nair_1 but more calls. Also similar to PfGCH1_dup_8 Pf3D7_12_v3 969921 969921 978641 978641 PF3D7_1223700 PF3D7_1224100 Nair 8.7kb GCH1 PfGCH1_Nair_3 GCH1 0 The 5' breakpoint is in the intron of VIT (vacuolar iron transporter) Pf3D7_12_v3 968861 968861 976141 976141 PF3D7_1223700 PF3D7_1224000 Nair 7.2kb GCH1 PfGCH1_Nair_4 GCH1 0 Similar to PfGCH1_dup_9 Pf3D7_07_v3 398869 398898 421765 421808 PF3D7_0708900 PF3D7_0709300 SCO1-MED14 CRT_dup_1 CRT 1 Pf3D7_07_v3 399263 399291 422103 422136 PF3D7_0708900 PF3D7_0709300 SCO1-MED14-Laos CRT_dup_2 CRT 1 Pf3D7_07_v3 390397 390416 421765 421808 PF3D7_0708700 PF3D7_0709300 COX4-MED14 CRT_dup_3 CRT 1 Pf3D7_07_v3 393103 393133 421765 421808 PF3D7_0708800 PF3D7_0709300 HSP110-MED14 CRT_dup_4 CRT 1 Pf3D7_07_v3 365968 365991 425216 425236 PF3D7_0707900 PF3D7_0709400 S8e-Cg7 CRT_dup_5 CRT 1