Table 3.
Summary of all genes containing mutations in the cutaneous isolates and classification into clusters.
| Cluster Number | Cluster Mutation Type | New annotation | Equivalents (when available) |
|---|---|---|---|
| Cluster 1 (13) | Nonsense, Frameshift, Insertions, Deletions, IV to VL | LdCL_300021700 | LdBPK_301640 |
| LdCL_310020800 | LdBPK_311390 | ||
| LdCL_250013200 | LdBPK_250790 | ||
| LdCL_310020100 | LdBPK_311320 | ||
| LdCL_310022200 | LdBPK_311510 | ||
| LdCL_080011700 | LdBPK_080670 | ||
| LdCL_340029800 | LdBPK_342210 | ||
| LdCL_230014900 | LdBPK_230830 | ||
| LdCL_310037100 | LdBPK_312870 | ||
| LdCL_220015800 | — | ||
| LdCL_140017600 | — | ||
| LdCL_230017500 | — | ||
| LdCL_310041200 | LdBPK_313290 | ||
| Cluster 2 (9) | Multiple SNPs in the same gene, Non-conservative amino acid change in conserved region with good PROVEAN score | LdCL_270015000 | LdBPK_270840 |
| LdCL_290026900 | LdBPK_292100 | ||
| LdCL_310021600 | LdBPK_311470 | ||
| LdCL_310028800 | LdBPK_312080 | ||
| LdCL_340046300 | LdBPK_343690 | ||
| LdCL_290022800 | LdBPK_291720 | ||
| LdCL_310024300 | LdBPK_311710 | ||
| LdCL_360006000 | LdBPK_360120 | ||
| LdCL_360062000 | LdBPK_365480 | ||
| Cluster 3 (18) | Non-conservative amino acid change in conserved region with poor PROVEAN score | LdCL_070018300 | LdBPK_071330 |
| LdCL_320013800 | LdBPK_320820 | ||
| LdCL_250016900 | LdBPK_251150 | ||
| LdCL_220022000 | LdBPK_221470 | ||
| LdCL_250015300 | LdBPK_251000 | ||
| LdCL_040011100 | LdBPK_040560 | ||
| LdCL_360016300 | LdBPK_361120 | ||
| LdCL_200014300 | LdBPK_200960 | ||
| LdCL_090011700 | LdBPK_090660 | ||
| LdCL_130016200 | LdBPK_131090 | ||
| LdCL_340009000 | LdBPK_340390 | ||
| LdCL_130017800 | LdBPK_131230 | ||
| LdCL_230009900 | LdBPK_230440 | ||
| LdCL_220018100 | LdBPK_221070 | ||
| LdCL_340044900 | LdBPK_343550 | ||
| LdCL_290028400 | — | ||
| LdCL_250011400 | LdBPK_250620 | ||
| LdCL_270014900 | LdBPK_270830 | ||
| Cluster 4 (8) | Conservative amino acid change in conserved region with good PROVEAN score | LdCL_350013100 | LdBPK_350830 |
| LdCL_360052700 | LdBPK_364550 | ||
| LdCL_230026600 | LdBPK_231940 | ||
| LdCL_230009400 | LdBPK_230400 | ||
| LdCL_320031100 | LdBPK_322560 | ||
| LdCL_020008200 | LdBPK_020280 | ||
| LdCL_310027700 | LdBPK_311990 | ||
| LdCL_320031200 | LdBPK_322570 | ||
| Cluster 5 (13) | Conservative amino acid change in conserved region with poor PROVEAN score | LdCL_330011900 | LdBPK_330640 |
| LdCL_170010200 | LdBPK_170470 | ||
| LdCL_070011900 | LdBPK_070700 | ||
| LdCL_210025000 | LdBPK_211930 | ||
| LdCL_290022900 | LdBPK_291730 | ||
| LdCL_200006300 | LdBPK_200140 | ||
| LdCL_290029000 | LdBPK_292290 | ||
| LdCL_030007500 | LdBPK_030250 | ||
| LdCL_250006200 | LdBPK_250110 | ||
| LdCL_360015800 | LdBPK_361070 | ||
| LdCL_310023400 | LdBPK_311630 | ||
| LdCL_360062700 | LdBPK_365540 | ||
| LdCL_140017700 | LdBPK_141190 | ||
| Cluster 6 (14) | Non-conservative amino acid change in less conserved region, Conservative amino acid change in less conserved region | LdCL_340022100 | LdBPK_341580 |
| LdCL_060011600 | LdBPK_060650 | ||
| LdCL_210015400 | LdBPK_211040 | ||
| LdCL_050010900 | LdBPK_050580 | ||
| LdCL_230011600 | LdBPK_230610 | ||
| LdCL_250024100 | LdBPK_251840 | ||
| LdCL_070015100 | LdBPK_071060 | ||
| LdCL_250005300 | LdBPK_250040 | ||
| LdCL_310022100 | LdBPK_311500 | ||
| LdCL_200006800 | LdBPK_200200 | ||
| LdCL_250014400 | LdBPK_250910 | ||
| LdCL_230010400 | LdBPK_230500 | ||
| LdCL_120008300 | LdBPK_120275 | ||
| LdCL_290028100 | LdBPK_292210 | ||
| Cluster 7 (4) | IV-only mutations | LdCL_140010000 | LdBPK_140470 |
| LdCL_310035800 | LdBPK_312770 | ||
| LdCL_310036400 | LdBPK_312810 | ||
| LdCL_320046000 | LdBPK_324000 | ||
| LdCL_360021300 | LdBPK_361580 | ||
| LdCL_360021400 | LdBPK_361590 | ||
| LdCL_360021500 | LdBPK_361600 | ||
| LdCL_360021600 | LdBPK_361610 |
Entries were not repeated in multiple lists.
Identified mutations were further classified into priority clusters for effect on protein function and future analysis for genes associated with survival in visceral organs. Mutations were prioritized by likelihood of contributing to visceral tissue tropism by severity of the coding change, accumulation of secondary mutations and conservation. Gene loci listed from the current assembly as well as previous ID numbers when available.