Spreadsheet: 30e042b8-0d89-4799-b76f-7c8f56a63681
Sheet: Sheet1

Table S6. Genetic variability among TPE (CDC-2, Samoa D and [NAME]) strains genomes. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14 | Unnamed: 15 | Unnamed: 16 | Unnamed: 17 | Unnamed: 18 | Unnamed: 19 | Unnamed: 20 | Unnamed: 21 | Unnamed: 22 | Unnamed: 23 | Unnamed: 24 | Unnamed: 25 | Unnamed: 26 | Unnamed: 27 | Unnamed: 28 | Unnamed: 29
COORDINATES (AE000520) | AE000520 | COORDINATES CDC-2 | CDC-2 | COORDINATES Samoa D | Samoa D | COORDINATES Gauthier | [NAME] | TYPE OF CHANGE (coding/intergenic) | AA CHANGE | cons/noncons | [NAME] (SamoaD) | SNP_AA (CDC-2) | SNP_AA ([NAME]) | AA POSITION (Samoa D proteins) | GENE POSITION (Samoa D genes) | LOCUS TAG in Samoa D ([NAME]) | START | END | [NAME] | GENOME WITH DIFERENCE IN SEQUENCE | GENE ENDs | GENOME WITH DIFERENCE IN GENE ENDs | PRODUCT | FUNCTION | UPSTREAM_LOCUS_TAG | UPSTREAM_DISTANCE | DOWNSTREAM_LOCUS_TAG | DOWNSTREAM_DISTANCE | NOTES
8213 | G | 8214 | G | 8214 | G | 8214 | A | coding | NON | noncons | D | D | N | 401 | 1201 | TPESAMD_0006 (TP0006-TP0007-TP0008) | 7014 | 8261 | plus | [NAME] | same |  | conserved hypothetical protein | unknown
9782 | G | 9785 | G | 9785 | A | 9785 | G | coding | NON | noncons | L | P | P | 128 | 383 | TPESAMD_0009 | 8344 | 10167 | minus | Samoa D | same |  | [NAME] protein A | unknown
27863 | G | 27871 | G | 27871 | G | 27871 | A | coding | NON | noncons | V | V | I | 103 | 307 | TPESAMD_0023 | 27565 | 28896 | plus | [NAME] | same |  | NSS family probable amino acid:sodium (Na+) symporter | transport
41220 | T | 41225 | C | 41225 | T | 41225 | T | coding | NON | noncons | I | V | I | 176 | 526 | TPESAMD_0033 | 41082 | 41750 | minus | CDC-2 | same |  | conserved hypothetical membrane protein | unknown
46983-46984 | 2 T | 46988-46989 | 2 T | 46988-46989 | 2 T | 46988 | T | coding | frameshift |  | I | I | -* | 15 | 44-45 | TPESAMD_0040 | 46945 | 49389 | plus | [NAME] | 129 nts, 43 aa shorter | [NAME] | probable methyl-accepting chemotaxis protein | cell processes |  |  |  |  | * protein is shorter because of T deletion
54508 | G | 54513 | C | 54513 | G | 54512 | G | intergenic | SNP |  |  |  |  |  |  |  |  |  |  | CDC-2 |  |  |  |  | [NAME] (+) | 26 | TP0045 (-) | 30
58873 | G | 58879 | A | 58879 | G | 58878 | G | coding | SYN |  | Y | Y | Y | 185 | 555 | TPESAMD_0050 | 58825 | 59433 | minus | CDC-2 | same |  | possible phosphoribosyltransferase | general metabolism
73404-73720 | ins 303 bp | 73402-73718 | ins 303 bp | 73402-73415 | del 303 bp | 73401-73717 | ins 303 bp | coding | INS |  | - | ins 101 aa | ins 101 aa | 248-254 | 747-760 | TPESAMD_0067 | 72656 | 73525 | plus | Samoa D | same |  | conserved hypothetical protein | unknown |  |  |  |  | became TPR domain protein in CDC-2 and Gauthier, *
77460 | G | 77458 | G | 77155 | G | 77457 | A | coding | SYN |  | H | H | H | 361 | 1083 | TPESAMD_0071 | 75601 | 78237 | minus | [NAME] | same |  | S14 family endopeptidase ClpB | cell processes
80253 | T | 80251 | T | 79948 | C | 80250 | T | coding | NON | noncons | R | H | H | 126 | 377 | TPESAMD_0073 | 78783 | 80324 | minus | Samoa D | same |  | conserved hypothetical protein | unknown
101949 | C | 101952 | G | 101649 | C | 101951 | C | coding | NON | noncons | H | D | H | 128 | 382 | TPESAMD_0092 | 101268 | 101810 | plus | CDC-2 | same |  | DNA-directed [NAME] polymerase sigma subunit RpoE | transcription
106878 | T | 106881 | C | 106578 | T | 106880 | T | coding | NON | noncons | D | G | D | 164 | 491 | TPESAMD_0098 | 106412 | 107068 | minus | CDC-2 | same |  | [NAME] | cell processes
124647 | T | 124647 | T | 124344 | A | 124646 | T | intergenic | SNP |  |  |  |  |  |  |  |  |  |  | Samoa D |  |  |  |  | TP0109 (-) | 7 | TP0110 (+) | 534
136547 | T | 136547 | C | 136244 | T | 136546 | C | coding | NON | noncons | K | E | E | 51 | 151 | TPESAMD_0117 | 134598 | 136394 | minus | Samoa D | same |  | [NAME] protein C | unknown
136727-136736 | 10 C | 136727-136736 | 10 C | 136424-136433 | 10 C | 136726-136734 | 9 C | intergenic | DEL |  |  |  |  |  |  |  |  |  |  | [NAME] |  |  |  |  | TP0117 (-) | 30-39 | TP0118 (-) | 50-41
148340-148349 | 10 C | 148340-148348 | 9 C | 148037-148046 | 10 C | 148338-148346 | 9 C | coding | frameshift |  |  |  |  | 217-214 | 649-640 | TPESAMD_0126 (+tprK-like) | 147309 | 148685 | minus | Samoa D | 725 nts, 242 aa longer | Samoa D | treponemal conserved hypothetical membrane protein | unknown |  |  |  |  | creating two genes in CDC-2 nad [NAME] strains
151098 | T | 152343 | C | 152041 | C | 152341 | T | intergenic | SNP |  |  |  |  |  |  |  |  |  |  | [NAME] |  |  |  |  | TP0130 (-) | 69 | TP0131 (-) | 3
151122 | G | 152367 | A | 152065 | A | 152365 | G | coding | SYN |  | C | C | C | 590 | 1770 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] | same |  | [NAME] protein D | unknown
151130 | G | 152375 | G | 152073 | G | 152373 | A | coding | NON | noncons | L | L | F | 588 | 1762 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown
151163 | C | 152408 | C | 152106 | C | 152406 | G | coding | NON | noncons | E | E | Q | 577 | 1729 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown
151164 | G | 152409 | G | 152107 | G | 152407 | A | coding | NON | noncons | A | A | T | 576 | 1728 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown
151166 | C | 152411 | C | 152109 | C | 152409 | T | coding | NON | noncons | A | A | T | 576 | 1726 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown
151170 | G | 152415 | G | 152113 | G | 152413 | A | coding | SYN |  | G | G | G | 574 | 1722 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown
151272-151344 | TCGTTCATTCAACAGGTTGCCCGCGGGGTTAATAATGTTAAAGCGATTGGTTGTGCCGAGCACGGATGTGTGT | 152517-152589 | GTGCTCACGCAGGAGCGCATCCCCGCTCTGGTTGTGGTTGAAGCGGTTTGTTGCCCATAGCACGGATGTGTGT | 152215-152287 | GTGCTCACGCAGGAGCGCATCCCCGCTCTGGTTGTGGTTGAAGCGGTTTGTTGCCCATAGCACGGATGTGTGT | 152515-152587 | TCGTTCATTCACCAGGTTGCCCGCGGCGTTAATAATGTTAAAGCGATTGGTTGTGCCGAGCACGGATGTGTGC | coding | SSSSSSNNSSSSSNNNNNNNSNNSN | ------nn-----nncncnn-nn-n | PHTSVLWATNRFNHNQSGDALLREH | PHTSVLWATNRFNHNQSGDALLREH | PHTSVLGTTNRFNIINAAGNLVNER | 540-516 | 1620-1548 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown |  |  |  |  | 24 SNPs + 2 times del of 1 bp  and once ins of 2 bp ????
151395-151475 | CTTCCCCAAAATTGGCATATTGATAGTCCCAGGGGGCACAGCTCCATTCAGTTCGTACCCTCCGTTATTTCTGTAACGGAT | 152640-152720 | TTTGCTCAAGATAGGCGTGTTGATGACGCCGTCCGAATTACTTCCCTTGTACTGCGCACCTCCGTTATTTATGTAAAAGAT | 152338-152418 | TTTGCTCAAGATAGGCGTGTTGATGACGCCGTCCGAATTACTTCCCTTGTACTGCGCACCTCCGTTATTTATGTAAAAGAT | 152638-152718 | CTTCCCCAAAATCGGCATATTGATAGTCCCAGAGGGCACAACTCCATTCAGTGGGTACCCTCCGTTATTTTTGTAAAAGAC | coding | NSSNSSSSNNNNSNNNNSNSSNSSSNS | n--n----nnnn-nnnn-n--n---n- | IFYINNGGAQYKGSNSDGVINTPILSK | IFYINNGGAQYKGSNSDGVINTPILSK | VFYKNNGGYPLNGVVPSGTINMPILGK | 499-473 | 1497-1417 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown |  |  |  |  | 24 SNPs + 2 times del of 1 bp  and 2 times ins of 1 bp ????
151554 | T | 152799 | C | 152497 | C | 152797 | T | coding | SYN |  | K | K | K | 446 | 1338 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown
151557 | G | 152802 | A | 152500 | A | 152800 | G | coding | SYN |  | T | T | T | 445 | 1335 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown
151592-151623 | AGTGCGCACGAGTGGTAGCAAAGACGCGTTTG | 152837-152868 | GATCTGCTTGATTCTTAAAGAAAACACGTTCT | 152535-152566 | GATCTGCTTGATTCTTAAAGAAAACACGTTCT | 152835-152866 | AGTGCGCACGAGTGGTAGCAAAGACGCGTTTG | coding | SNSSSNNNNSNN | -N---nnnn-nn | GERVFFKNQADH | GERVFFKNQADH | GKRVFATTRAHY | 434-423 | 1300-1269 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown |  |  |  |  | 16 SNPs
151662 | A | 152907 | A | 152605 | A | 152905 | G | coding | SYN |  | S | S | S | 410 | 1230 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown
151675 | T | 152920 | C | 152618 | C | 152918 | T | coding | NON | cons | R | R | K | 406 | 1217 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown
151688 | G | 152933 | C | 152631 | C | 152931 | G | coding | NON | noncons | G | G | R | 402 | 1204 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown
151712-152051 | CGTTCATAGGTGCGCGCTCAAGGAAAGCGAGAAGTTTAGCAGTGACAACTCTTGGATCGGAAGAGCGGAAGACATCACGTACTCCTTGCTCTATGTTCGGTACAAGTTGCGATACAAGCGCCGCGAGCGCGCCAGCGGCTAGCACGGTTTGAATGGCGCTGCCGAGCGTTCCTTCTGCAATCAAAGCAGCAAGTCCTACCATCTCTATGAGAGTGGTTTGTTCGGTGATTCCTGGTGGCATCATGATATTGGGAAGGTTCTGCACGAGTTTCCCCTCCACCCGTCTAAACACTTCCCTTGCTTTGAGGATAGCTCTCTCTTGGGTCTGAGCATGTGCGTT | 152957-153290 | TTTTGGTGTACGTGAATTGCAACCAGGAAATAAAGAGTGCTGTCCGCATCCGCGCGTCAGGATTCTTCTGCTGCTCTATGAGCCTCATGTTTATTTCTAGGCCTTTGCCATTCAGATGTCTTAGGTAACCACCGCTTGACGCTAAGCCGACGATGGTGCGCTGCGCCAAGAGCGTTACTAAGCCAGCTTTCTCCAGAAGACTGCCTTTGCTCAGTTCTTGCACAAAGAATGAAACAACATCTTGTTGCGGGGAGGTCAGCAGCGTGTCCCCAAGACTATTGATGACTTCATGGACCCTCTGTGAGGGAGCCATTCTAAAGTAGAATTTTGTGTC | 152655-152989 | TTTTGGTGTACGTGAATTGCAACCAGGAAATAAAGAGTGCTGTCCGCATCCGCGCGTCAGGATTCTTCTGCTGCTCTATGAGCCTCATGTTTATTTCTAGGCCTTTGCCATTCAGATGTCTTAGGTAACCACCGCTTGACGCTAAGCCGACGATGGTGCGCTGCGCCAAGAGCGTTACTAAGCCAGCTTTCTCCAGAAGACTGCCTTTGCTCAGTTCTTGCACAAAGAATGAAACAACATCTTGTTGCGGGGAGGTCAGCAGCGTGTCCCCAAGACTATTGATGACTTCATGGACCCTCTGTGAGGGAGCCATTCTAAAGTAGAATTTTGTGTC | 152955-153294 | CGTTCATAGGTGCGCGCTCAAGGAAAGCGAGAAGTTTAGCAGTGACAACTCTTGGATCGGAAGAGCGGAAGACATCACGTACTCCTTGCTCTATGTGCGGTACAAGTTGCGATACAAGCGCCGCGAGCGCGCCAGCGGCTAGCACGGTTTGAATGGCGCTGCCGAGCGTTCCTTCTGCAATCAAAGCAGCAAGTCCTACCATCTCTATGAGAGTGGTTTGTTCGGTGATTCCTAGTGGCATCATGATATTGGGAAGGTTCTGCACGAGTTTCCCCACCACCTGTCCAAACACTTCCCCTGCGAGGCTAACTCTCTCTTTTTGGGTCTGAGCATCTGCGTT | coding | 95 SNP, 2 DEL, 4 INZ |  | DTKFYFRMAPSQRVHEVINSLGDTLLTSPQQDVVSFFVQELSKGSLLEKAGLVTLLAQ----RTIVGLASSGGYLRHLNGKGLEINMRLIEQQKNPDARMRTALFISWLQFTYTKT | DTKFYFRMAPSQRVHEVINSLGDTLLTSPQQDVVSFFVQELSKGSLLEKAGLVTLLAQ----RTIVGLASSGGYLRHLNGKGLEINMRLIEQQKNPDARMRTALFISWLQFTYTKT | NADAQTQKERVSLAGEVFGQVVGKLVQNLPNIMMPLGITEQTTLIEMVGLAALIAEGTLGSAIQTVLAAGALAALVSQLV | 394-283 | 1180-847 | TPESAMD_0131 | 152044 | 153834 | minus | [NAME] |  |  | [NAME] protein D | unknown |  |  |  |  | 113 SNPs + 20 times ins of 1 bp + 2 times ins of 2 bp + 2 times ins of 3 bp + 15  times del of 1 bp + 3 times del od 2 bp + del of 3 bp  ?????????
152747 | T | 153986 | C | 153684 | T | 153990 | T | coding | NON | noncons | K | E | K | 51 | 151 | TPESAMD_0131 | 152044 | 153834 | minus | CDC-2 |  |  | [NAME] protein D | unknown
152927-152935 | 9 C | 154166-154174 | 9 C | 153864-153873 | 10 C | 154170-154178 | 9 C | intergenic | INS |  |  |  |  |  |  |  |  |  |  | Samoa D |  |  |  |  | TP0131 (-) | 30-39 | TP0133 (-) | 171-162
157063 | C | 158200 | C | 157899 | C | 158204 | T | coding | NON | noncons | S | S | F | 91 | 272 | TPESAMD_0136 | 157628 | 159040 | plus | [NAME] | same |  | treponemal conserved hypothetical outer membrane protein | virulence
TP0136 | G | 158344 | G | 158043 | T | 158348 | G | coding | NON | noncons | I | S | S | 139 | 416 | TPESAMD_0136 | 157628 | 159040 | plus | Samoa D |  |  | treponemal conserved hypothetical outer membrane protein | virulence
157274 | G | 158408 | G | 158107 | T | 158412 | G | coding | NON | noncons | C | W | W | 160 | 480 | TPESAMD_0136 | 157628 | 159040 | plus | Samoa D |  |  | treponemal conserved hypothetical outer membrane protein | virulence
157339-157459 | ins 63 bp | 158473-158563 | ins 33 bp | 158172-158229 | del 33 bp | 158477-158534 | del 33 bp | coding | INS |  | ----------- | ins IRITDSSSSSC | ----------- | 182-201 | 545-602 | TPESAMD_0136 | 157628 | 159040 | plus | CDC-2 |  |  | treponemal conserved hypothetical outer membrane protein | virulence
157354 | C | 158488 (158521) | C | 158187 | T | 158492 | C | coding | NON | noncons | L | S | S | 187 | 560 | TPESAMD_0136 | 157628 | 159040 | plus | Samoa D |  |  | treponemal conserved hypothetical outer membrane protein | virulence
157432 | C | 158503 (158536) | C | 158202 | C | 158507 | T | coding | NON | noncons | T | T | I | 192 | 575 | TPESAMD_0136 | 157628 | 159040 | plus | [NAME] |  |  | treponemal conserved hypothetical outer membrane protein | virulence
158514 | T | 159609 | G | 159275 | G | 159580 | A | coding | SYN |  | A | A | A | 40 | 120 | TPESAMD_0136a | 159156 | 159347 | plus | [NAME] | same |  | hypothetical protein | unknown
163496 | G | 164591 | G | 164257 | G | 164562 | A | coding | NON | cons | A | A | V | 445 | 1334 | TPESAMD_0143 | 163809 | 165590 | minus | [NAME] | same |  | ABC superfamily ATP binding cassette transporter, membrane protein | transport
197278 | C | 198372 | C | 198038 | T | 198343 | C | coding | NON | noncons | E | G | G | 435 | 1304 | TPESAMD_0179 | 197392 | 199341 | minus | Samoa D | same |  | treponemal conserved hypothetical protein | unknown
205534 | G | 206629 | G | 206295 | A | 206600 | G | coding | NON | noncons | D | G | G | 180 | 539 | TPESAMD_0189 | 205757 | 206383 | plus | Samoa D | same |  | ribosomal protein L3 | translation
207435-207442 | 8 G | 208530-208539 | 10 G | 208196-208203 | 8 G | 208501-208509 | 9 G | intergenic | INDEL |  |  |  |  |  |  |  |  |  |  | all |  |  |  |  | TP0192 (+) | 1-8 | TP0193 (+) | 9-2 | heterogeneity in CDC-2
209230 | A | 210327 | G | 209991 | A | 210297 | A | coding | NON | cons | K | R | K | 129 | 386 | TPESAMD_0196 | 209606 | 210025 | plus | CDC-2 | same |  | ribosomal protein L16 | translation
223749 | A | 224849 | A | 224513 | A | 224819 | G | coding | NON | noncons | R | R | G | 26 | 76 | TPESAMD_0219 | 224438 | 226585 | plus | [NAME] | same |  | probable sigma factor regulatory protein | regulation
224907 | G | 226007 | G | 225671 | G | 225977 | A | coding | NON | noncons | E | E | K | 412 | 1234 | TPESAMD_0219 | 224438 | 226585 | plus | [NAME] |  |  | probable sigma factor regulatory protein | regulation
231764-231827 | tRNA-Ile | 232867-232940 | tRNA-Ala + 4 bp noncoding | 232531-232594 | tRNA-Ile | 232837-232910 | tRNA-Ala + 4 bp noncoding | intergenic | INS |  |  |  |  |  |  | tRNA-Ile |  |  | plus | Samoa D | same |  |  |  |  |  |  |  | inversion
242734 | T | 243848 | C | 243502 | T | 243818 | T | coding | NON | noncons | I | T | I | 79 | 236 | TPESAMD_0236 | 243267 | 243824 | plus | CDC-2 | same |  | transcription antitermination protein NusG | regulation
245574-245579 | 6 G | 246688-246693 | 6 G | 246342-246347 | 6 G | 246658-246664 | 7 G | intergenic |  |  |  |  |  |  |  |  |  |  |  | [NAME] |  |  |  |  | TP0240.1 (+) | 45-50 | TP0241 (+) | 11-6
253236 | G | 254350 | A | 254004 | G | 254321 | G | coding | NON | noncons | R | Q | R | 1368 | 4103 | TPESAMD_0242 | 249902 | 254152 | plus | CDC-2 | same |  | DNA-directed RNA polymerase subunit beta prime | transcription
269959 | T | 271072 | C | 270726 | T | 271043 | T | coding | SYN |  | T | T | T | 26 | 78 | TPESAMD_0258 | 270093 | 270803 | minus | CDC-2 | same |  | conserved hypothetical protein | unknown
270349-270366 | ins 9 bp | 271462-271479 | ins 9 bp | 271116-271133 | ins 9 bp | 271433-271441 | del 9 bp | coding | DEL |  | EPQ | EPQ | --- | 79-85 | 235-252 | TPESAMD_0259 | 270882 | 271493 | plus | [NAME] | same |  | conserved hypothetical protein | unknown |  |  |  |  | deletion of 3 aminoacids
280198-280271 | tRNA-Ala + 4 bp noncoding | 281279-281342 | tRNA-Ile | 280933-281006 | tRNA-Ala + 4 bp noncoding | 281241-281304 | tRNA-Ile | intergenic |  |  |  |  |  |  |  | tRNA-Ala + 4 bp noncoding |  |  | plus | Samoa D | same |  |  |  |  |  |  |  | inversion
291799 | T | 292870 | T | 292534 | C | 292832 | T | coding | SYN |  | T | T | T | 193 | 579 | TPESAMD_0276 | 292273 | 293112 | minus | Samoa D | same |  | possible RNA methyltransferas | general metabolism
294937 | T | 296009 | T | 295673 | T | 295971 | C | coding | NON | noncons | L | L | S | 232 | 695 | TPESAMD_0279 | 294979 | 297570 | plus | [NAME] | same |  | bifunctional cytidylate kinase/ribosomal protein S1 | translation
325846 | G | 326917 | G | 326581 | A | 326879 | G | coding | NON | noncons | H | R | R | 81 | 242 | TPESAMD_0309 | 326340 | 327158 | plus | Samoa D | same |  | probable polar amino acid ABC superfamily ATP binding cassette transporter, binding protein | transport
330072 | T | 331143 | T | 330807 | C | 331105 | C | coding | SYN |  | G | G | G | 696 | 2088 | TPESAMD_0313 | 328720 | 331008 | plus | CDC-2 | same |  | [NAME] protein E | unknown
330301 | G | 331372 | G | 331036 | A | 331334 | A | intergenic | SNP |  |  |  |  |  |  |  |  |  |  | CDC-2 |  |  |  |  | TP0313 (+) | 28 | TP0315 (-) | 28
330308 | T | 331379 | T | 331043 | C | 331341 | C | intergenic | SNP |  |  |  |  |  |  |  |  |  |  | CDC-2 |  |  |  |  | TP0313 (+) | 35 | TP0315 (-) | 21
331257 | G | 332958 | A | 332622 | G | 332920 | G | coding | NON | noncons | R | W | R | 360 | 1078 | TPESAMD_0316 | 331870 | 333699 | minus | CDC-2 |  |  | [NAME] protein F | unknown
331714 | G | 333415 | G | 333079 | A | 333377 | G | coding | SYN |  | F | F | F | 207 | 621 | TPESAMD_0316 | 331870 | 333699 | minus | Samoa D |  |  | [NAME] protein F | unknown
331726 | G | 333427 | G | 333091 | A | 333389 | G | coding | SYN |  | S | S | S | 203 | 609 | TPESAMD_0316 | 331870 | 333699 | minus | Samoa D |  |  | [NAME] protein F | unknown
331737 | T | 333438 | T | 333102 | G | 333400 | T | coding | NON | noncons | P | T | T | 200 | 598 | TPESAMD_0316 | 331870 | 333699 | minus | Samoa D |  |  | [NAME] protein F | unknown
332594 | A | 334296 | A | 333960 | G | 334258 | A | coding | SYN |  | G | G | G | 690 | 2070 | TPESAMD_0317 | 333759 | 336029 | minus | Samoa D | same |  | [NAME] protein G | unknown
332803 | C | 334505 | C | 334169 | T | 334467 | C | coding | NON | noncons | M | V | V | 621 | 1861 | TPESAMD_0317 | 333759 | 336029 | minus | Samoa D |  |  | [NAME] protein G | unknown
332876 | A | 334578 | G | 334242 | A | 334540 | G | coding | SYN |  | L | L | L | 596 | 1788 | TPESAMD_0317 | 333759 | 336029 | minus | Samoa D |  |  | [NAME] protein G | unknown
334673-334683 | 11 C | 336375-336385 | 11 C | 336039-336048 | 10 C | 336337-336347 | 11 C | intergenic | DEL |  |  |  |  |  |  |  |  |  |  | Samoa D |  |  |  |  | TP0317 (-) | 10-19 | TP0319 (+) | 149-140 | heterogeneity in CDC-2
336437 | G | 338139 | G | 337802 | A | 338101 | G | coding | NON | noncons | K | E | E | 105 | 313 | TPESAMD_0321 | 337490 | 339091 | plus | Samoa D | same |  | sugar ABC superfamily ATP binding cassette transporter, ABC protein | transport
338786-338787 | del C | 340488-340490 | ins C | 340151-340152 | del C | 340450-340451 | del C | coding | SNNNNNNNNNS | -nnncnnnnn- | NGIRAMLVRWG | NWNPGDARQVG | NGIRAMLVRWG | 384-394 | 1151-1152 | TPESAMD_0322 | 339001 | 340203 | plus | CDC-2 | same |  | sugar ABC superfamily ATP binding cassette transporter, membrane protein | transport
338813-338817 | 5 G | 340516-340519 | 4 G | 340178-340182 | 5 G | 340477-340481 | 5 G | coding | SNNNNNNNNNS | -nnncnnnnn- | NGIRAMLVRWG | NWNPGDARQVG | NGIRAMLVRWG | 384-394 | 1178-1182 | TPESAMD_0322 | 339001 | 340203 | plus | CDC-2 |  |  | sugar ABC superfamily ATP binding cassette transporter, membrane protein | transport
342702 | C | 344405 | T | 344068 | C | 344367 | C | coding | NON | noncons | P | S | P | 939 | 2815 | TPESAMD_0324 (TP0324-TP0325) | 341254 | 345660 | plus | CDC-2 | same |  | treponemal conserved hypothetical outer membrane protein | unknown
345876 | A | 347579 | A | 347242 | A | 347541 | G | coding | NON | noncons | Y | Y | C | 518 | 1553 | TPESAMD_0326 | 345690 | 348191 | plus | [NAME] | same |  | outer membrane protein | virulence
346241 | T | 347944 | T | 347607 | T | 347906 | C | coding | NON | noncons | F | F | L | 640 | 1918 | TPESAMD_0326 | 345690 | 348191 | plus | [NAME] |  |  | outer membrane protein | virulence
346386 | G | 348089 | G | 347752 | T | 348051 | G | coding | NON | noncons | L | R | R | 688 | 2063 | TPESAMD_0326 | 345690 | 348191 | plus | Samoa D |  |  | outer membrane protein | virulence
346396-346403 | GAAAACG | 348099-348106 | GAAAGG---- | 347762-347772 | AAAAAAAAT | 348061-348068 | GAAGAG--- | coding | NON NON DEL | noncons cons/noncons - | KKN | ER- | EE- | 691-695 | 2073-2083 | TPESAMD_0326 | 345690 | 348191 | plus | all |  |  | outer membrane protein | virulence
347956 | G | 349644 | A | 349310 | G | 349606 | G | coding | SYN |  | E | E | E | 163 | 489 | TPESAMD_0328 | 348822 | 351524 | plus | CDC-2 | same |  | DNA mismatch repair protein MutS | DNA replication, repair, recombination
366703 | A | 368390 | G | 368056 | A | 368352 | A | coding | NON | noncons | I | T | I | 1060 | 3179 | TPESAMD_0344 | 367812 | 371234 | minus | CDC-2 | same |  | transcription-repair coupling factor | DNA replication, repair, recombination
366819 | A | 368506 | A | 368172 | A | 368468 | G | coding | SYN |  | Y | Y | Y | 1021 | 3063 | TPESAMD_0344 | 367812 | 371234 | minus | [NAME] |  |  | transcription-repair coupling factor | DNA replication, repair, recombination
371576 | C | 373263 | T | 372929 | C | 373225 | C | coding | NON | noncons | R | C | R | 99 | 295 | TPESAMD_0346 | 372635 | 373336 | plus | CDC-2 | same |  | conserved hypothetical protein | unknown
371655 | A | 373342 | G | 373008 | A | 373304 | A | coding | NON | noncons | Q | R | Q | 125 | 374 | TPESAMD_0346 | 372635 | 373336 | plus | CDC-2 |  |  | conserved hypothetical protein | unknown
383963 | A | 385650 | A | 385316 | A | 385612 | G | coding | SYN |  | V | V | V | 38 | 114 | TPESAMD_0362 | 385203 | 385439 | plus | [NAME] | same |  | ribosomal protein L28 | translation
387307 | C | 388994 | C | 388660 | T | 388956 | C | coding | NON | noncons | S | P | P | 100 | 298 | TPESAMD_0364 | 388363 | 389730 | plus | Samoa D | same |  | chemotaxis protein CheW | regulation
426484 | A | 428173 | A | 427839 | A | 428135 | G | coding | NON | noncons | H | H | R | 136 | 407 | TPESAMD_0401 | 427433 | 428362 | plus | [NAME] | same |  | IIISP family [NAME] (virulence-related) secretory pathway protein | virulence
433689 | G | 435377 | G | 435043 | G | 435339 | A | coding | SYN |  | R | R | R | 659 | 1977 | TPESAMD_0408 | 433067 | 436321 | plus | [NAME] | same |  | conserved hypothetical protein | unknown
446337 | C | 448028 | C | 447694 | T | 447990 | C | coding | SYN |  | H | H | H | 199 | 597 | TPESAMD_0418 | 447098 | 448291 | plus | Samoa D | same |  | galactokinase | general metabolism
461078-461508 | 7 repetitions | 462763-463012 | [NAME] bp, 4 repetitions | 462429-463158 | 12 repetitions | 462725-463334 | del120 bp, 10 repetitions | coding | DEL |  | 240 aa | del 160 aa - 8 rep. | del 40 aa  - 2 rep. | 182-425 | 546-1275 | TPESAMD_0433 (TP0433-TP0434) | 461884 | 463578 | plus | all | same |  | treponemal conserved hypothetical protein | unknown |  |  |  |  | rep.:  EDVPKVVEPASEREGGEREV
464468 | C | 465972 | C | 466118 | T | 466294 | C | coding | NON | noncons | F | L | L | 79 | 235 | [NAME] | 465884 | 466693 | plus | Samoa D | same |  | HAM1 protein | general metabolism
468510 | C | 470014 | C | 470160 | T | 470336 | C | coding | SYN |  | L | L | L | 241 | 721 | TPESAMD_0442 | 469440 | 471161 | plus | Samoa D | same |  | DNA repair protein RecN | DNA replication, repair, recombination
490812-490821 | 10 C | 492316-492325 | 10 C | 492462-492471 | 10 C | 492638-492646 | 9 C | coding | frameshift |  |  |  |  | 113-116/  46-43 | 337-346 /137-128 | TPESAMD_0461 TPESAMD_0461a | 492126 492416 | 492485 492598 | plus minus | [NAME] | 27 nts, 9 aa shorter at N-end,  frameshift - 31 nts, 10 aa longer at C-end -TP0461/ frameshift - 61 nts, 20 aa longer, at C-end -TP0461.1 | [NAME] | probable transcriptional regulator hypothetical protein | regulation unknown
497264-497691 | 17 repetitions | 498748-499655 | ins 600 bp, 37 repetitions | 498894-499201 | 12 repetions | 499069-499688 | ins 312 bp, 25 repetitions | coding | INS |  | 96 aa | ins 200 aa - 25 rep | ins 112 aa - 14 rep. | 294-191 | 880-573 | TPESAMD_0470 | 498784 | 499773 | minus | all | same |  | conserved hypothetical protein | unknown |  |  |  |  | rep.: EARRKEAE
508822 | T | 510787 | T | 510333 | C | 510820 | T | coding | NON | noncons | V | I | I | 4 | 10 | TPESAMD_0478 | 508795 | 510342 | minus | Samoa D | same |  | glucose-6-phosphate 1-dehydrogenase | general metabolism
509476-509484 | 9 C | 511441-511449 | 9 C | 510987-510995 | 9 C | 511474-511483 | 10 C | coding | frameshift |  |  |  |  | 34-32 | 103-95 | TPESAMD_0479 | 510415 | 511089 | minus | [NAME] | 135 nts,  45 aa shorter at N-end,  frameshift | [NAME] | hypothetical membrane protein | unknown
511981 | A | 513947 | G | 513493 | A | 513980 | A | coding | SYN |  | S | S | S | 591 | 1773 | TPESAMD_0481 (TP0481-TP0482) | 511721 | 513970 | plus | CDC-2 | same |  | hypothetical protein | unknown
520844 | C | 522811 | C | 522357 | C | 522845 | T | coding | SYN |  | V | V | V | 127 | 381 | TPESAMD_0487 | 520581 | 522737 | minus | [NAME] | same |  | treponemal conserved hypothetical protein | unknown
521430 | T | 523397 | C | 522943 | T | 523431 | T | coding | NON | noncons | I | T | I | 186 | 557 | [NAME] | 522387 | 524924 | plus | CDC-2 | same |  | methyl-accepting chemotaxis protein | cell processes
521480 | A | 523447 | G | 522993 | A | 523481 | A | coding | NON | noncons | I | V | I | 203 | 607 | [NAME] | 522387 | 524924 | plus | CDC-2 |  |  | methyl-accepting chemotaxis protein | cell processes
521570 | G | 523537 | C | 523083 | G | 523571 | G | coding | NON | noncons | A | P | A | 233 | 697 | [NAME] | 522387 | 524924 | plus | CDC-2 |  |  | methyl-accepting chemotaxis protein | cell processes
521588 | A | 523555 | A | 523101 | G | 523589 | A | coding | NON | noncons | E | K | K | 239 | 715 | [NAME] | 522387 | 524924 | plus | Samoa D |  |  | methyl-accepting chemotaxis protein | cell processes
521693 | A | 523660 | C | 523206 | A | 523694 | A | coding | NON | noncons | K | Q | K | 274 | 820 | [NAME] | 522387 | 524924 | plus | CDC-2 |  |  | methyl-accepting chemotaxis protein | cell processes
521760 | A | 523727 | A | 523273 | A | 523761 | G | coding | NON | noncons | D | D | G | 296 | 887 | [NAME] | 522387 | 524924 | plus | [NAME] |  |  | methyl-accepting chemotaxis protein | cell processes
521771 | A | 523738 | A | 523284 | A | 523772 | G | coding | NON | noncons | I | I | V | 300 | 898 | [NAME] | 522387 | 524924 | plus | [NAME] |  |  | methyl-accepting chemotaxis protein | cell processes
521871 | T | 523838 | T | 523384 | T | 523872 | C | coding | NON | noncons | F | F | S | 333 | 998 | [NAME] | 522387 | 524924 | plus | [NAME] |  |  | methyl-accepting chemotaxis protein | cell processes
522086 | A | 524053 | G | 523599 | A | 524087 | A | coding | NON | noncons | I | V | I | 405 | 1213 | [NAME] | 522387 | 524924 | plus | CDC-2 |  |  | methyl-accepting chemotaxis protein | cell processes
522525 | A | 524492 | A | 524038 | A | 524526 | G | coding | NON | noncons | H | H | R | 551 | 1652 | [NAME] | 522387 | 524924 | plus | [NAME] |  |  | methyl-accepting chemotaxis protein | cell processes
531734 | A | 533708 | A | 533254 | A | 533742 | G | coding | NON | noncons | E | E | G | 283 | 848 | TPESAMD_0496 | 532407 | 533396 | plus | [NAME] | same |  | conserved hypothetical membrane protein | unknown
532506 | G | 534480 | G | 534026 | A | 534514 | G | coding | SYN |  | Q | Q | Q | 206 | 618 | TPESAMD_0497 | 533409 | 534443 | plus | Samoa D | same |  | cell shape determining protein MreB | cell processes
539199 | G | 541173 | G | 540719 | G | 541207 | A | coding | NON | noncons | R | R | C | 400 | 1198 | TPESAMD_0505 | 540582 | 541916 | minus | [NAME] | same |  | hexokinase | general metabolism
547150 | T | 549124 | T | 548670 | C | 549158 | T | coding | SYN |  | G | G | G | 85 | 255 | TPESAMD_0511 | 548416 | 549147 | plus | Samoa D | same |  | CarD family transcriptional regulator | regulation
550930 | G | 552904 | G | 552450 | G | 552938 | A | coding | NON | noncons | V | V | M | 158 | 472 | TPESAMD_0514 | 551979 | 554861 | plus | [NAME] | same |  | excision endonuclease subunit UvrA | DNA replication, repair, recombination
565828 | C | 567803 | G | 567349 | C | 567837 | C | coding | SYN |  | V | V | V | 490 | 1470 | TPESAMD_0524 | 566173 | 568818 | minus | CDC-2 | same |  | S16 family endopeptidase La | cell processes
569160 | C | 571135 | C | 570681 | T | 571169 | C | coding | SYN |  | G | G | G | 339 | 1017 | TPESAMD_0526 | 569665 | 571671 | plus | Samoa D | same |  | ATP-dependent helicase HrpA | DNA replication, repair, recombination
573652 | C | 575627 | T | 575173 | C | 575661 | C | coding | NON | noncons | G | D | G | 176 | 527 | TPESAMD_0529 | 573882 | 575699 | minus | CDC-2 | same |  | two-sector ATPase, V(1) subunit A | transport
5736374 | A | 578350 | A | 577896 | A | 578384 | G | coding | SYN |  | Y | Y | Y | 252 | 756 | TPESAMD_0533 | 576966 | 578651 | minus | [NAME] | same |  | two-sector ATPase, V(0) subunit I | transport
581626 | G | 583605 | G | 583151 | A | 583639 | G | intergenic | SNP |  |  |  |  |  |  |  |  |  |  | Samoa D |  |  |  |  | TP0538.2 (+) | 21 | TP0540 (+) | 68
589711 | G | 591696 | G | 591242 | G | 591730 | A | coding | NON | noncons | T | T | I | 233 | 698 | TPESAMD_0546 | 590224 | 591939 | minus | [NAME] | same |  | S1B subfamily peptidase | general metabolism
590842 | C | 592827 | C | 592373 | T | 592861 | C | coding | NON | noncons | T | A | A | 232 | 694 | TPESAMD_0547 | 591936 | 593066 | minus | Samoa D | same |  | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | general metabolism
591829 | G | 593812 | G | 593358 | T | 593846 | G | coding | NON | noncons | L | R | R | 50 | 149 | TPESAMD_0548 | 593210 | 594508 | plus | Samoa D | same |  | treponemal conserved hypothetical membrane protein | unknown
591840 | T | 593821 | A | 593367 | A | 593855 | G | coding | NON | noncons | E | E | G | 53 | 158 | TPESAMD_0548 | 593210 | 594508 | plus | [NAME] |  |  | treponemal conserved hypothetical membrane protein | unknown
591847 | G | 593826 | G | 593372 | A | 593860 | T | coding | NON | noncons | N | G | C | 55 | 163 | TPESAMD_0548 | 593210 | 594508 | plus | all |  |  | treponemal conserved hypothetical membrane protein | unknown
591848 | G | 593827 | G | 593373 | A | 593861 | G | coding | NON | noncons | N | G | C | 55 | 164 | TPESAMD_0548 | 593210 | 594508 | plus | Samoa D |  |  | treponemal conserved hypothetical membrane protein | unknown
591850 | A | 593829 | G | 593375 | A | 593863 | G | coding | NON | noncons | S | G | G | 56 | 166 | TPESAMD_0548 | 593210 | 594508 | plus | Samoa D |  |  | treponemal conserved hypothetical membrane protein | unknown
591857 | G | 593836 | G | 593382 | A | 593870 | A | coding | NON | noncons | D | G | D | 58 | 173 | TPESAMD_0548 | 593210 | 594508 | plus | CDC-2 |  |  | treponemal conserved hypothetical membrane protein | unknown
592117 | T | 594096 | T | 593642 | A | 594130 | T | coding | NON | cons | T | S | S | 145 | 433 | TPESAMD_0548 | 593210 | 594508 | plus | Samoa D |  |  | treponemal conserved hypothetical membrane protein | unknown
592159 | G | 594138 | A | 593684 | A | 594172 | G | coding | NON | noncons | S | S | G | 159 | 475 | TPESAMD_0548 | 593210 | 594508 | plus | [NAME] |  |  | treponemal conserved hypothetical membrane protein | unknown
592162 | A | 594141 | T | 593687 | A | 594175 | A | coding | NON | noncons | N | C | S | 160 | 478 | TPESAMD_0548 | 593210 | 594508 | plus | CDC-2 |  |  | treponemal conserved hypothetical membrane protein | unknown
592163 | A | 594142 | G | 593688 | A | 594176 | G | coding | NON | noncons | N | C | S | 160 | 479 | TPESAMD_0548 | 593210 | 594508 | plus | Samoa D |  |  | treponemal conserved hypothetical membrane protein | unknown
592171 | G | 594150 | G | 593696 | G | 594184 | A | coding | NON | noncons | G | G | S | 163 | 487 | TPESAMD_0548 | 593210 | 594508 | plus | [NAME] |  |  | treponemal conserved hypothetical membrane protein | unknown
592174 | G | 594153 | A | 593699 | G | 594187 | G | coding | NON | noncons | G | K | G | 164 | 490 | TPESAMD_0548 | 593210 | 594508 | plus | CDC-2 |  |  | treponemal conserved hypothetical membrane protein | unknown
592175 | G | 594154 | A | 593700 | G | 594188 | G | coding | NON | noncons | G | K | G | 164 | 491 | TPESAMD_0548 | 593210 | 594508 | plus | CDC-2 |  |  | treponemal conserved hypothetical membrane protein | unknown
592307 | A | 594286 | A | 593832 | G | 594320 | A | coding | NON | noncons | G | D | D | 208 | 623 | TPESAMD_0548 | 593210 | 594508 | plus | Samoa D |  |  | treponemal conserved hypothetical membrane protein | unknown
592442 | G | 594421 | G | 593967 | A | 594455 | G | coding | NON | noncons | D | G | G | 253 | 758 | TPESAMD_0548 | 593210 | 594508 | plus | Samoa D |  |  | treponemal conserved hypothetical membrane protein | unknown
592624 | G | 594603 | A | 594149 | A | 594637 | G | coding | NON | noncons | K | K | E | 314 | 940 | TPESAMD_0548 | 593210 | 594508 | plus | [NAME] |  |  | treponemal conserved hypothetical membrane protein | unknown
592634 | C | 594613 | C | 594159 | T | 594647 | C | coding | NON | cons | V | A | A | 317 | 950 | TPESAMD_0548 | 593210 | 594508 | plus | Samoa D |  |  | treponemal conserved hypothetical membrane protein | unknown
593213 | C | 595244 | C | 594790 | C | 595278 | T | coding | NON | noncons | R | R | C | 45 | 133 | TPESAMD_0549 | 594658 | 597102 | plus | [NAME] | same |  | S14 family endopeptidase ClpA | cell processes
593344 | A | 595375 | A | 594921 | C | 595409 | A | coding | NON | noncons | N | K | K | 88 | 264 | TPESAMD_0549 | 594658 | 597102 | plus | Samoa D |  |  | S14 family endopeptidase ClpA | cell processes
598358 | C | 600389 | T | 599935 | C | 600423 | C | coding | NON | noncons | V | I | V | 112 | 334 | TPESAMD_0552 | 599735 | 600268 | minus | CDC-2 | same |  | treponemal conserved hypothetical protein | unknown
618479 | G | 620511 | G | 620057 | G | 620545 | A | coding | NON | noncons | S | S | L | 339 | 1016 | TPESAMD_0569 | 618748 | 621072 | minus | [NAME] | same |  | Xaa-Pro aminopeptidase | general metabolism
634125 | A | 636170 | A | 635716 | A | 636204 | G | coding | NON | noncons | T | T | A | 94 | 280 | TPESAMD_0584 | 635437 | 636846 | plus | [NAME] | same |  | treponemal conserved hypothetical protein | unknown
634379 | A | 636424 | A | 635970 | G | 636458 | A | coding | SYN |  | A | A | A | 178 | 534 | TPESAMD_0584 | 635437 | 636846 | plus | Samoa D | same |  | treponemal conserved hypothetical protein | unknown
654065 | A | 656113 | A | 655659 | A | 656147 | G | coding | SYN |  | F | F | F | 282 | 846 | TPESAMD_0602 | 655641 | 656504 | minus | [NAME] | same |  | phosphatidate cytidylyltransferase | general metabolism
671810 | G | 673855 | A | 673401 | G | 673889 | G | coding | NON | noncons | R | W | R | 360 | 1078 | TPESAMD_0620 | 672649 | 674478 | minus | CDC-2 | same |  | [NAME] protein I | unknown
672267 | G | 674312 | G | 673858 | A | 674346 | G | coding | SYN |  | F | F | F | 207 | 621 | TPESAMD_0620 | 672649 | 674478 | minus | Samoa D |  |  | [NAME] protein I | unknown
672279 | G | 674324 | G | 673870 | A | 674358 | G | coding | SYN |  | S | S | S | 203 | 609 | TPESAMD_0620 | 672649 | 674478 | minus | Samoa D |  |  | [NAME] protein I | unknown
672290 | T | 674335 | T | 673881 | G | 674369 | T | coding | NON | noncons | P | T | T | 200 | 598 | TPESAMD_0620 | 672649 | 674478 | minus | Samoa D |  |  | [NAME] protein I | unknown
672917-672924 | 8 C | 674962-674970 | 9 C | 674508-674516 | 9 C | 674996-675005 | 10 C | intergenic | INS |  |  |  |  |  |  |  |  |  |  | [NAME] |  |  |  |  | TP0620 (-) | 30-38 | TP0621 (-) | 29-21
673146 | A | 675192 | A | 674738 | G | 675227 | A | coding | SYN |  | G | G | G | 690 | 2070 | TPESAMD_0621 | 674537 | 676807 | minus | Samoa D | same |  | [NAME] protein J | unknown
673355 | C | 675401 | C | 674947 | T | 675436 | C | coding | NON | noncons | M | V | V | 621 | 1861 | TPESAMD_0621 | 674537 | 676807 | minus | Samoa D |  |  | [NAME] protein J | unknown
673428 | A | 675474 | G | 675020 | A | 675509 | G | coding | SYN |  | L | L | L | 596 | 1788 | TPESAMD_0621 | 674537 | 676807 | minus | Samoa D |  |  | [NAME] protein J | unknown
675283 | A | 677323 | A | 676869 | A | 677358 | G | coding | NON | noncons | stop | stop | Q* | -* | 1780 | TPESAMD_0622 | 676867 | 678648 | minus | [NAME] | 6 nts, 2 aa longer | [NAME] | treponemal conserved hypothetical membrane protein | unknown |  |  |  |  | *read through the stopcodon
676731 | A | 678771 | G | 678317 | A | 678806 | A | coding | NON | noncons | L | P | L | 111 | 332 | TPESAMD_0622 | 676867 | 678648 | minus | CDC-2 |  |  | treponemal conserved hypothetical membrane protein | unknown
680791 | G | 682831 | G | 682377 | A | 682866 | G | coding | SYN |  | K | K | K | 180 | 540 | TPESAMD_0625 | 681838 | 682590 | plus | Samoa D | same |  | treponemal conserved hypothetical protein | unknown
686989-687300 | ins 302 bp | 689029-689340 | ins 302 bp | 688575-688886 | ins 302 bp | 689064-689073 | del 302 bp | coding | frameshift |  |  |  |  | 5-108 | 13-324 | TPESAMD_0629 | 688563 | 689375 | plus | [NAME] | 357 nts, 119 aa shorter | [NAME] | treponemal conserved hypothetical protein | unknown
698794 | G | 700835 | G | 700381 | G | 700568 | A | coding | NON | noncons | V | V | I | 348 | 1042 | TPESAMD_0639 | 699340 | 701274 | plus | [NAME] | same |  | methyl-accepting chemotaxis protein | cell processes
715724 | G | 717767 | G | 717313 | A | 717500 | G | coding | SYN |  | M | M | M | 1 | 1 | TPESAMD_0652 | 717313 | 718440 | plus | Samoa D | same |  | spermidine/putrescine ABC superfamily ATP binding cassette transporter, ABC protein | transport |  |  |  |  | [NAME] still OK
716646 | A | 718689 | G | 718235 | A | 718422 | A | coding | NON | noncons | N | S | N | 308 | 923 | TPESAMD_0652 | 717313 | 718440 | plus | CDC-2 |  |  | spermidine/putrescine ABC superfamily ATP binding cassette transporter, ABC protein | transport
718061 | T | 720104 | T | 719650 | C | 719837 | T | coding | NON | noncons | H | Y | Y | 108 | 322 | TPESAMD_0654 | 719329 | 720147 | plus | Samoa D | same |  | spermidine/putrescine ABC superfamily ATP binding cassette transporter, membrane protein | transport
742832 | A | 744869 | A | 744415 | A | 744602 | G | coding | NON | noncons | T | T | A | 68 | 202 | TPESAMD_0678 | 744214 | 745137 | plus | [NAME] | same |  | treponemal conserved hypothetical protein | unknown
766238 | C | 768275 | C | 767821 | C | 768008 | G | coding | NON | cons | G | G | A | 29 | 86 | TPESAMD_0698 | 767361 | 767906 | minus | [NAME] | same |  | hypothetical membrane protein | unknown
775502 | C | 777540 | C | 777086 | C | 777273 | T | coding | SYN |  | Y | Y | Y | 62 | 186 | TPESAMD_0708 | 776901 | 777416 | plus | [NAME] | same |  | hypothetical protein | unknown
780468 | C | 782506 | T | 782052 | C | 782239 | C | coding | SYN |  | V | V | V | 337 | 1011 | TPESAMD_0713 | 781749 | 783062 | minus | CDC-2 | same |  | flagellar-associated GTP-binding protein FlhF | cell structure
809516 | C | 811555 | C | 811101 | T | 811288 | C | coding | NON | noncons | T | A | A | 754 | 2260 | TPESAMD_0746 | 810655 | 813360 | minus | Samoa D | same |  | pyruvate, phosphate dikinase | general metabolism
811186 | G | 813225 | G | 812771 | G | 812958 | A | coding | NON | cons | A | A | V | 197 | 590 | TPESAMD_0746 | 810655 | 813360 | minus | [NAME] |  |  | pyruvate, phosphate dikinase | general metabolism
812002 | G | 814041 | A | 813587 | G | 813774 | G | coding | NON | noncons | S | L | S | 273 | 818 | TPESAMD_0747 | 813370 | 814404 | minus | CDC-2 | same |  | treponemal conserved hypothetical protein | unknown
829437 | G | 831477 | G | 831023 | G | 831210 | A | coding | SYN |  | S | S | S | 372 | 1116 | [NAME] | 829958 | 832138 | minus | [NAME] | same |  | [NAME] family endopeptidase FtsH | cell processes
876677 | T | 878717 | T | 878263 | C | 878450 | C | coding | NON | noncons | R | H | R | 193 | 578 | TPESAMD_0806 | 877344 | 878840 | minus | CDC-2 | same |  | [NAME] family protein | cell structure
931906 | G | 933948 | G | 933494 | A | 933681 | G | coding | NON | noncons | F | L | L | 354 | 1060 | TPESAMD_0855 | 931170 | 934553 | minus | Samoa D | same |  | treponemal conserved hypothetical outer membrane protein | unknown
934563 | A | 936609 | A | 936155 | G | 936342 | A | coding | NON / NON | noncons / noncons | P / R | L / Q | L / Q | 343 54 | 1028 161 | TPESAMD_0856a TPESAMD_0858 | 935812 935995 | 937182 937224 | minus plus | Samoa D | 606 nts, 202 aa shorter, frameshift, TP0856.1 | [NAME] | hypothetical protein treponemal conserved hypothetical protein | unknown unknown
934575 | A | 936621 | A | 936167 | A | 9360354 | G | coding | NON / NON | noncons / noncons | L / Q | L / Q | P / R | 339 58 | 1016 173 | TPESAMD_0856a TPESAMD_0858 | 935812 935995 | 937182 937224 | minus plus | [NAME] |  |  | hypothetical protein treponemal conserved hypothetical protein | unknown unknown
934753 | C | 936799 | C | 936345 | C | 936532 | T | coding | NON / SYN | noncons / | E/L | E/L | K/L | 280 117 | 838 351 | TPESAMD_0856a TPESAMD_0858 | 935812 935995 | 937182 937224 | minus plus | [NAME] |  |  | hypothetical protein treponemal conserved hypothetical protein | unknown unknown
934756 | T | 936802 | T | 936348 | T | 936535 | C | coding | NON / SYN | noncons / | R/S | R/S | G/S | 279 118 | 835 354 | TPESAMD_0856a TPESAMD_0858 | 935812 935995 | 937182 937224 | minus plus | [NAME] |  |  | hypothetical protein treponemal conserved hypothetical protein | unknown unknown
934769 | T | 936815 | T | 936361 | T | 936548 | C | coding | NON / NON | noncons / noncons | R/S | R/S | P/R | 274/123 | 822 /367 | TPESAMD_0856a TPESAMD_0858 | 935812 935995 | 937182 937224 | minus plus | [NAME] |  |  | hypothetical protein treponemal conserved hypothetical protein | unknown unknown
934770 | C | 936816 | C | 936362 | C | 936549 | G | coding | NON / NON | noncons / noncons | R/S | R/S | P/R | 274/123 | 821 /368 | TPESAMD_0856a TPESAMD_0858 | 935812 935995 | 937182 937224 | minus plus | [NAME] |  |  | hypothetical protein treponemal conserved hypothetical protein | unknown unknown
935234 | A | 937283 | A | 936829 | G | 937016 | C | coding | SYN -* / NON | / noncons | F / E | F / K | -* / Q | 118 279 | 354 835 | TPESAMD_0856a TPESAMD_0858 | 935812 935995 | 937182 937224 | minus plus | all |  |  | hypothetical protein treponemal conserved hypothetical protein | unknown unknown |  |  |  |  | * deletion in Gauthier genome sequence causes frameshift and protein shortening, it is not possible to describe this change in protein
935475-935571 | G + ins 79 bp | 937521-937617 | G + ins 79 bp | 937067-937163 | G + ins 79 bp | 937254-937271 | A + del 79 bp | coding | -*/ NON,frameshift | / noncons,frameshift | S/G | S/G | -*/R | 39-7 / 358-390 | 116-20/ 1073-1169 | TPESAMD_0856a TPESAMD_0858 | 935812 935995 | 937182 937224 | minus plus | [NAME] | 606 nts, 202 aa shorter, frameshift, TP0856.1/gene end - 7 nts longer, frameshift - different length - whole protein is 24 aa shorter    TP0858 | [NAME] | hypothetical protein treponemal conserved hypothetical protein | unknown unknown |  |  |  |  | *deletion in Gauthier genome sequence causes frameshift and protein shortening, it is not possible to describe this change in protein
936262 | C | 938308 | C | 937854 | C | 937962 | A | coding | SYN |  | R | R | R | 183 | 549 | TPESAMD_0859-TPESAMD_0860 | 937306 | 938805 | plus | [NAME] | same |  | treponemal conserved hypothetical protein | unknown
943727 | T | 945785 | T | 945331 | C | 945439 | C | coding | NON | noncons | S | N | S | 361 | 1082 | TPESAMD_0865 | 944967 | 946412 | minus | CDC-2 | same |  | treponemal conserved hypothetical membrane protein | unknown
944086-944087 | del 9 bp | 946150 | G | 945696 | C | 945804 | G | coding | NON | cons | E | D | D | 239 | 717 | TPESAMD_0865 | 944967 | 946412 | minus | Samoa D |  |  | treponemal conserved hypothetical membrane protein | unknown
944089 | G | 946153 | G | 945699 | G | 945807 | T | coding | NON | noncons | N | N | K | 238 | 714 | TPESAMD_0865 | 944967 | 946412 | minus | [NAME] |  |  | treponemal conserved hypothetical membrane protein | unknown
944507 | T | 946571 | C | 946117 | T | 946225 | C | coding | NON | noncons | E | G | G | 99 | 296 | TPESAMD_0865 | 944967 | 946412 | minus | Samoa D |  |  | treponemal conserved hypothetical membrane protein | unknown
956866 | G | 958932 | G | 958478 | A | 958586 | G | coding | SYN |  | R | R | R | 114 | 342 | TPESAMD_0879 | 957338 | 958819 | minus | Samoa D | same |  | conserved hypothetical membrane protein | unknown
1018272 | C | 1020365 | C | 1019969 | T | 1020034 | C | coding | NON | noncons | N | D | D | 136 | 406 | TPESAMD_0936 | 1019301 | 1020374 | minus | Samoa D | same |  | probable hemolysin | cell processes
1041816 | C | 1043911 | T | 1043515 | C | 1043580 | C | coding | NON | noncons | V | M | V | 161 | 481 | TPESAMD_0960 | 1043201 | 1043995 | minus | CDC-2 | same |  | flagellar basal body rod protein FlgG | cell structure
1047711 | T | 1049806 | T | 1049410 | T | 1049475 | C | coding | NON | noncons | N | N | D | 485 | 1453 | TPESAMD_0966 | 1049228 | 1050862 | minus | [NAME] | same |  | treponemal conserved hypothetical protein | unknown
1049168-1049173 | 6 C | 1051263-1051268 | 6 C | 1050867-1050872 | 6 C | 1050932-1050940 | 9 C | intergenic | INS |  |  |  |  |  |  |  |  |  |  | [NAME] |  |  |  |  | TP0966 (-) | 5-10 | TP0967 (-) | 42-37
1050284-1050311 | ins 18 bp | 1052379-1052418 | ins 18 bp | 1051983-1052004 | del 18 bp | 1052051-1052090 | ins 18 bp | coding | DEL |  | ------ | GGGGGG | GGGGGG | 159-151 | 474-453 | TPESAMD_0967 | 1050909 | 1052456 | minus | Samoa D | same |  | treponemal conserved hypothetical protein | unknown
1050294 | C | 1052383 | G | 1051987 | G | 1052055 | C | coding | NON | cons | A | A | G | 157 | 470 | TPESAMD_0967 | 1050909 | 1052456 | minus | [NAME] |  |  | treponemal conserved hypothetical protein | unknown
1050296 | T | 1052385 | C | 1051989 | C | 1052057 | T | coding | SYN |  | G | G | G | 156 | 468 | TPESAMD_0967 | 1050909 | 1052456 | minus | [NAME] |  |  | treponemal conserved hypothetical protein | unknown
1056967 | C | 1059074 | T | 1058660 | C | 1058746 | C | coding | NON | noncons | R | C | R | 207 | 619 | TPESAMD_0973 | 1058042 | 1059691 | plus | CDC-2 | same |  | phenylalanine--tRNA ligase alpha subunit | translation
1060023 | G | 1062129 | A | 1061715 | G | 1061801 | G | coding | NON | noncons | G | S | G | 257 | 769 | TPESAMD_0976 | 1060947 | 1062326 | plus | CDC-2 | same |  | hypothetical membrane protein | unknown
1065808 | G | 1067914 | G | 1067500 | C | 1067586 | G | coding | NON | noncons | L | V | V | 176 | 526 | TPESAMD_0982 | 1066975 | 1067601 | plus | Samoa D | same |  | rhomboid family protein | general metabolism
1070550-1070557 | 8 G | 1072656-1072664 | 9 G | 1072242-1072250 | 9 G | 1072328-1072337 | 10 G | intergenic | INS |  |  |  |  |  |  |  |  |  |  | [NAME] |  |  |  |  | TP0985 (+) | 40-48 | TP0986 (+) | 17-9
1078468 | T | 1080576 | C | 1080162 | T | 1080249 | T | coding | NON | noncons | T | A | T | 95 | 283 | TPESAMD_0993a | 1080148 | 1080444 | minus | CDC-2 | same |  | hypothetical protein | unknown
1088568 | G | 1090677 | G | 1090263 | T | 1090350 | G | intergenic | SNP |  |  |  |  |  |  |  |  |  |  | Samoa D |  |  |  |  | TP0999 (+) | 122 | TP1000 (+) | 56
1098897 | G | 1101006 | G | 1100592 | A | 1100679 | G | coding | SYN |  | S | S | S | 544 | 1632 | TPESAMD_1008 | 1099686 | 1102223 | minus | Samoa D | same |  | ribonucleotide-diphosphate reductase subunit alpha | general metabolism
1103333 | C | 1105442 | C | 1105028 | C | 1105115 | T | coding | NON | noncons | G | G | R | 215 | 643 | TPESAMD_1012 | 1104735 | 1105670 | minus | [NAME] | same |  | DNA-directed [NAME] polymerase sigma subunit RpoD | transcription
1109560 | G | 1111669 | G | 1111255 | G | 1111342 | A | coding | SYN |  | V | V | V | 65 | 195 | TPESAMD_1017 | 1109632 | 1111449 | minus | [NAME] | same |  | alanine--tRNA ligase | translation
1124596 | T | 1126329 | C | 1125915 | T | 1126002 | T | coding | SYN |  | Y | Y | Y | 123 | 369 | TPESAMD_1031 | 1125547 | 1127217 | plus | CDC-2 | same |  | [NAME] protein L | unknown
1125250 | C | 1126983 | C | 1126569 | T | 1126656 | C | coding | SYN |  | L | L | L | 341 | 1023 | TPESAMD_1031 | 1125547 | 1127217 | plus | Samoa D |  |  | [NAME] protein L | unknown
1127044 | C | 1128777 | C | 1128363 | T | 1128450 | C | coding | NON | noncons | R | G | G | 102 | 304 | TPESAMD_1033 | 1127731 | 1128666 | minus | Samoa D | same |  | [NAME] family phospholipase | general metabolism
1128848 | C | 1130581 | C | 1130167 | C | 1130254 | T | coding | SYN |  | Q | Q | Q | 822 | 2466 | TPESAMD_1035 | 1129762 | 1132632 | minus | [NAME] | same |  | valine--tRNA ligase | translation
1130257 | G | 1131990 | G | 1131576 | G | 1131663 | A | coding | NON | noncons | R | R | W | 353 | 1057 | TPESAMD_1035 | 1129762 | 1132632 | minus | [NAME] |  |  | valine--tRNA ligase | translation