Table 1. Ancient genome order of last common ancestor (A16) of H. pylori.
| A16 order | J99 as reference | A16 order | HPAG1 as reference | A16 order | P12 as reference | A16 order | Shi470 as reference |
| 1b | Jhp_0001-jhp_0021 | 2 | HPAG1_0001-HPAG1_0023 | 1 | HPP12_0001-HPP12_0021 | 1 | HPSH_00005-HPSH_00120 |
| 2 | jhp_0022-jhp_0042 | 3 | HPAG1_0024-HPAG1_0045 | 2 | HPP12_0022-HPP12_0043 | 2 | HPSH_00130-HPSH_00240 |
| 3 | jhp_0043-jhp_0298 | 4 | HPAG1_0046-HPAG1_0317 | 3 | HPP12_0044-HPP12_0312 | 3 | HPSH_00245-HPSH_01635 |
| 5 | Jhp_0301-Jhp_0330 | 5 | HPAG1_0321-HPAG1_0351 | 4 | HPP12_0315-HPP12_0350 | 4 | HPSH_01645- HPSH_01835 |
| 6 | Jhp_0333-Jhp_0413 | 6 | HPAG1_0354-HPAG1_0436 | 5 | HPP12_0352-HPP12_0433 | 5 | HPSH_01850-HPSH_02260 |
| 7 | Jhp_0414-jhp_0439 | 7 | HPAG1_0437-HPAG1_0463 | 6 | HPP12_0434-HPP12_0494 | 6 | HPSH_02265-HPSH_02405 |
| 8 | Jhp_0442-jhp_0556 | 8 | HPAG1_0466- HPAG1_0590 | 7 | HPP12_0498-HPP12_0618 | −14 | HPSH_04465-HPSH_03815 |
| 4 | Jhp_0299-jhp_0300 | 9 | HPAG1_0591-HPAG1_0594 | 8 | HPP12_0619-HPP12_0622 | −13 | HPSH_03810 HPSH_03805 |
| 9 | Jhp_0557-jhp_0628 | 10 | HPAG1_0595-HPAG1_0671 | 9 | HPP12_0623-HPP12_0700 | −12 | HPSH_03800- HPSH_03425 |
| -10a | Jhp_0638-jhp_0631 | 11 | HPAG1_0675-HPAG1_0682 | 10 | HPP12_0701-HPP12_0708 | −11 | HPSH_03405-HPSH_03365 |
| 11 | Jhp_0639-jhp_0658 | 12 | HPAG1_0684-HPAG1_0705 | 11 | HPP12_0709-HPP12_0729 | −10 | HPSH_03360-HPSH_03265 |
| -12 | Jhp_0661-jhp_0660 | -13 | HPAG1_0708-HPAG1_0707 | 12 | HPP12_0731- HPP12_0732 | −9 | HPSH_03250 -HPSH_03245 |
| 13 | Jhp_0663-jhp_0753 | 14 | HPAG1_0710-HPAG1_0802 | 13 | HPP12_0734- HPP12_0823 | −8 | HPSH_03230- HPSH_02725 |
| 14 | Jhp_0757-jhp_0812 | 15 | HPAG1_0804-HPAG1_0861 | 14 | HPP12_0825- HPP12_0878 | −7 | HPSH_02720-HPSH_02420 |
| 15 | Jhp_0815- jhp_0913 | 16 | HPAG1_0863-HPAG1_0960 | 15 | HPP12_0880- HPP12_0975 | 15 | HPSH_04655-HPSH_05170 |
| 16 | Jhp_0915 | 17 | HPAG1_0963 | 16 | HPP12_0979 | 16 | HPSH_05200 |
| 17 | 5S-Jph_1023 | 18 | HPAG1_r015S-HPAG1_1035 | 17 | HPP12_5S-HPP12_1062 | 17 | HPSH_5S-HPSH05635 |
| 18 | Jhp_1024-jhp_1197 | 19 | HPAG1_1036-HPAG1_1220 | 18 | HPP12_1063-HPP12_1242 | 18 | HPSH_05640- HPSH_06610 |
| 19 | Jhp_1198-jhp_1206 | -22 | HPAG1_1235-HPAG1_1227 | 19 | HPP12_1243-HPP12_1252 | 19 | HPSH_06615-HPSH_06655 |
| 20 | Jhp_1207 | -21 | HPAG1_1226 | 20 | HPP12_1253 | −20 | HPSH_06665 |
| 21 | Jhp_1210-jhp_1211 | -20 | HPAG1_1223-HPAG1_1222 | 21 | HPP12_1256-HPP12_1257 | 21 | HPSH_06670-HPSH_06675 |
| 22 | Jhp_1212- Jhp_1261 | 23 | HPAG1_1237- HPAG1_1289 | 22 | HPP12_1258- HPP12_1305 | 22 | HPSH_06685-HPSH_06935 |
| 23 | jhp_1262-jhp_1282 | 24 | HPAG1_1290-HPAG1_1311 | 23 | HPP12_1306-HPP12_1363 | 23 | HPSH_06950-HPSH_07060 |
| 24 | jhp_1284-jhp_1285 | 25 | HPAG1_1313-HPAG1_1316 | 24 | HPP12_1365-HPP12_1366 | 24 | HPSH_07085-HPSH_07095 |
| 25 | jhp_1286-jhp_1295 | 26 | HPAG1_1317-HPAG1_1327 | 25 | HPP12_1367-HPP12_1376 | 25 | HPSH_07100-HPSH_07150 |
| 26 | Jhp_1298- jhp_1320 | 27 | HPAG1_1330- HPAG1-1352 | 26 | HPP12_1379 -HPP12_1399 | 26 | HPSH_07170- HPSH_07270 |
| -27 | Jhp_1325-jhp-1322 | 28 | HPAG1_1353-HPAG1_1356 | 27 | HPP12_1400- HPP12_1403 | 27 | HPSH_07275- HPSH_07290 |
| 28 | Jhp_1327-jhp_1346 | 29 | HPAG1_1360- HPAG1_1379 | 28 | HPP12_1409 - HPP12_1430 | 28 | HPSH_07305- HPSH_07435 |
| 29 | Jhp_1347-jhp_1421 | -30 | HPAG1_1461- HPAG1_1383 | 29 | HPP12_1432-HPP12_1507 | 29 | HPSH_07445-HPSH_07875 |
| 30 | Jhp_1423-jhp_1436 | 31 | HPAG1_1464-HPAG1_1479 | 30 | HPP12_1509-HPP12_ 1522 | 30 | HPSH_07890- HPSH_ 07950 |
| 31 | Jhp_1438-jhp_ 1441 | 32 | HPAG1_1481-HPAG1_1484 | -31 | HPP12_1527 - HPP12_1524 | 31 | HPSH_07970-HPSH_ 07985 |
| 32 | Jhp_1444- jhp_1461 | -33 | HPAG1_1487- HPAG1_1504 | 32 | HPP12_1529-HPP12_ 1546 | 32 | HPSH_08005- HPSH_08100 |
| 33 | Jhp_1464- jhp_1492 | 34 | HPAG1_1505- HPAG1_ 1533 | 33 | HPP12_1548 – HPP12_1576 | 33 | HPSH_08110-HPSH_08250 |
| 34 | Jhp_1494 | 1 | HPAG1_1536 | 34 | HPP12_1580-HPP12_1581 | 34 | HPSH_08270-HPSH_08275 |
a. “-” indicates an inversion block.
b. All blocks on the same row are homologs.