Spreadsheet: 8a688a04-c1b0-4faf-8f65-e5fcb3e56df7
Sheet: Sheet1

Table S2. All putative rearrangements identified by unusual read pair organization (see [NAME]).
Chromosome | Starta | Endb | [NAME] | Type | Sal I | Belem | C08 | C127 | C15 | M08 | M15 | M19 | Brazil | India VII | Mauritania I | North Korea | Mismappingd | Annotation
vivax02 | 14100 | 18100 |  | Deletion | - | - | - | - | - | - | - | - | - | - | - | 5 | no | pseudogene
vivax02 | 20700 | 25600 |  | Deletion | - | 53 | 8 | 2 | 1 | 95 | 7 | 38 | 24 | 16 | 24 | 4 | yes | Vir cluster
vivax03 | 850600 | 856800 |  | Deletion | - | 21 | 80 | 536 | 38 | 120 | 70 | 72 | 104 | 25 | 241 | 242 | yes | Hypothetical proteins
vivax04 | 69000 | 79200 |  | Deletion | - | 446 | 284 | 627 | 107 | 628 | 238 | 402 | 350 | 156 | 670 | 493 | yes | Pv-fam-b cluster
vivax04 | 558300 | 599100 |  | Deletion | - | 1022 | 555 | 848 | 200 | 913 | 124 | 495 | 361 | 113 | 685 | 466 | yes | SERA cluster
vivax05 | 552500 | 566100 |  | Deletion | - | 58 | 45 | 176 | 4 | 44 | - | - | 27 | - | 6 | 74 | yes | no annotated gene
vivax05 | 895200 | 905300 |  | Deletion | - | 185 | 392 | 1520 | 128 | 523 | 234 | 411 | 38 | 162 | 250 | 306 | yes | RAD cluster
vivax05 | 1353500 | 1361000 |  | Deletion | - | - | 13 | 421 | - | 152 | 41 | 23 | 8 | 62 | 82 | 120 | yes | RBP2
vivax06 | 71800 | 74000 |  | Deletion | - | 116 | - | - | 4 | - | - | - | - | - | - | - | no | Phist protein
vivax07 | 1389900 | 1390900 |  | Deletion | - | - | - | - | - | - | 2 | - | - | - | - | - | ??? | no annotated gene
vivax09 | 1536000 | 1537600 |  | Deletion | - | - | - | - | - | - | - | - | - | - | - | 82 | no | no annotated gene
vivax10 | 1218000 | 1264500 |  | Deletion | - | 1115 | 1877 | 5011 | 505 | 2438 | 803 | 1531 | 1205 | 412 | 1876 | 2037 | yes | MSP3 cluster
vivax11 | 1022300 | 1028700 |  | Deletion | - | - | - | - | - | - | - | 4 | - | - | - | - | ??? | Hypothetical proteins
vivax12 | 762100 | 778800 |  | Deletion | - | 843 | 200 | 870 | 99 | 538 | 160 | 190 | 253 | 61 | 353 | 250 | yes | MSP7 cluster
vivax12 | 2640400 | 2641400 |  | Deletion | - | - | - | - | - | - | - | - | - | 3 | - | - | ??? | Hypothetical proteins
[NAME] | 1256100 | 1257900 |  | Deletion | - | - | - | 6 | - | - | - | - | - | - | - | - | yes | Ribosomal RNAs
vivax14 | 16600 | 20100 |  | Deletion | - | - | 9 | 5 | 5 | 2 | 6 | 27 | 15 | 12 | 22 | 16 | yes | Hypothetical proteins
vivax14 | 780100 | 781500 |  | Deletion | - | - | - | - | - | - | - | - | - | - | - | 20 | no | no annotated gene
vivax14 | 3061600 | 3069300 |  | Deletion | - | - | 7 | 81 | - | 52 | - | 62 | 15 | 27 | 18 | - | no | RBP2L
vivax02 | 20800 | 25500 |  | Duplication | - | 64 | 7 | 2 | 4 | 74 | - | 51 | 29 | 22 | 60 | 12 | yes | Vir genes
vivax03 | 850900 | 856700 |  | Duplication | - | 124 | 142 | 450 | 22 | 238 | 69 | 78 | 128 | 12 | 179 | 190 | yes | Hypothetical proteins
vivax03 | 1004100 | 1006300 |  | Duplication | - | - | - | - | - | - | - | 15 | 24 | - | - | - | yes | Vir genes
vivax04 | 69000 | 78900 |  | Duplication | - | 293 | 280 | 701 | 91 | 467 | 180 | 324 | 293 | 152 | 651 | 448 | yes | Pv-fam-b cluster
vivax04 | 554100 | 599000 |  | Duplication | - | 778 | 504 | 793 | 185 | 904 | 104 | 397 | 302 | 80 | 562 | 248 | yes | SERA cluster
vivax05 | 552500 | 555000 |  | Duplication | - | 129 | 33 | 143 | 10 | 27 | - | - | 10 | - | 4 | 68 | yes | no annotated gene
vivax05 | 895200 | 905200 |  | Duplication | - | 318 | 302 | 1040 | 114 | 239 | 159 | 314 | 41 | 94 | 282 | 320 | yes | RAD cluster
vivax05 | 1353700 | 1360800 |  | Duplication | - | - | 14 | 411 | - | 95 | 33 | 28 | 11 | 26 | 112 | 62 | yes | RBP2
vivax06 | 382600 | 390700 |  | Duplication | - | - | - | - | - | - | 21 | 2 | - | - | 3 | - | no | Duffy binding receptor
vivax10 | 1218200 | 1264200 |  | Duplication | - | 1370 | 1533 | 4726 | 486 | 2805 | 703 | 1443 | 1400 | 341 | 1723 | 2360 | yes | [NAME]
vivax12 | 762200 | 778600 |  | Duplication | - | 1138 | 251 | 1036 | 168 | 641 | 192 | 232 | 307 | 46 | 658 | 265 | yes | MSP7 Cluster
[NAME] | 646700 | 651700 |  | Duplication | - | - | 2 | - | - | - | - | - | - | - | - | - | yes | methionine aminopeptidase
vivax03 | 835900 | 848400 |  | Inversion | - | 491 | 412 | 1077 | 90 | 542 | 76 | 431 | 92 | 129 | 505 | 28 | yes | Hypothetical proteins
vivax05 | 651700 | 718400 |  | Inversion | - | - | - | - | - | - | - | 4 | - | - | - | - | yes | N/A
vivax05 | 826100 | 903900 |  | Inversion | - | - | - | 2 | - | - | - | - | - | - | - | - | yes | N/A
vivax09 | 1448600 | 1451000 |  | Inversion | - | - | - | 2 | - | - | - | - | - | - | - | - | yes
vivax11 | 589900 | 594200 |  | Inversion | - | - | 2 | 62 | 4 | 43 | - | 19 | 28 | 5 | - | - | yes | Elongation factor alpha
vivax12 | 1747100 | 1761600 |  | Inversion | - | - | - | 2 | - | - | - | - | - | - | - | - | yes
vivax14 | 2019300 | 2033000 |  | Inversion | - | 72 | - | 45 | - | - | 8 | - | - | - | 3 | 1 | yes | Hypothetical proteins
The table shows for each sample the number of read pairs in unusual configuration indicating putative DNA sequence rearrangements. Dashes (-) indicate that no read pairs supported a sequence rearrangement at this location.
a Upstream chromosomal coordinate of the sequence rearrangement based on the Sal I reference sequence.
b Downstream chromosomal coordinate of the sequence rearrangement based on the Sal I reference sequence.
c Nucleotide length of the sequence rearrangment
d Indicates whether the unusual read pairs is likely caused by mismapping of one of the reads due to high DNA sequence homology in this region.