Table 1 Characteristics of clinical H. pylori isolates and sequencing results
| Â | Strain | Diagnosis | Isolation | Total reads (before trimming) | Total reads (after trimming) | Total consensus length (bp) | Total consensus coverage (%) | Average coverage (fold) | Quality control |
|---|---|---|---|---|---|---|---|---|---|
1 | 174 | CG | Okinawa | 3,004,008 | 3,003,954 | 1,534,120 | 91.98 | 165.1 | Yes |
2 | 177 | CG | Okinawa | 2,619,844 | 2,591,582 | 1,656,888 | 99.34 | 101.2 | Yes |
3 | 179 | CG | Okinawa | 2,200,712 | 2,190,051 | 1,518,618 | 91.05 | 123.6 | Yes |
4 | 189 | CG | Okinawa | 2,010,838 | 1,989,271 | 1,651,152 | 99.00 | 79.5 | No |
5 | 194 | CG | Okinawa | 6,936,714 | 6,929,125 | 1,553,487 | 93.14 | 407.5 | No |
6 | S1 | GU | Kobe | 2,271,944 | 2,271,917 | 1,534,031 | 91.98 | 144.7 | Yes |
7 | S2 | CG | Kobe | 5,962,628 | 5,962,520 | 1,542,099 | 92.46 | 333.4 | Yes |
8 | S4 | CG | Kobe | 4,640,490 | 4,640,409 | 1,536,143 | 92.10 | 255.4 | Yes |
9 | S8 | CG | Kobe | 10,869,516 | 10,869,208 | 1,563,806 | 93.76 | 669.4 | Yes |
10 | S13 | CG | Kobe | 3,873,394 | 3,873,195 | 1,526,445 | 91.52 | 258.2 | Yes |
11 | S16 | CG | Kobe | 6,782,392 | 6,782,004 | 1,555,964 | 93.29 | 437.9 | Yes |
12 | S17 | GC | Kobe | 5,700,038 | 5,699,682 | 1,554,277 | 93.19 | 318.4 | Yes |
13 | S22 | GU | Kobe | 6,597,254 | 6,596,851 | 1,557,252 | 93.37 | 416.5 | Yes |
14 | S23 | CG | Kobe | 5,064,464 | 5,040,754 | 1,514,281 | 90.79 | 340.9 | Yes |
15 | S26 | CG | Kobe | 6,692,038 | 6,691,708 | 1,543,795 | 92.56 | 432.7 | Yes |
16 | F21 | GC | Fukui | 3,757,854 | 3,745,628 | 1,511,942 | 90.65 | 263.0 | Yes |
17 | F23 | CG | Fukui | 5,765,092 | 5,733,420 | 1,514,387 | 90.80 | 387.6 | Yes |
18 | F24 | DU | Fukui | 4,672,544 | 4,648,960 | 1,527,146 | 91.56 | 323.5 | Yes |
19 | F28 | DU | Fukui | 7,184,480 | 7,122,238 | 1,537,656 | 92.19 | 365.6 | Yes |
20 | F32 | GC | Fukui | 5,230,564 | 5,200,093 | 1,531,123 | 91.80 | 268.2 | Yes |
21 | F44 | DU | Fukui | 3,887,082 | 3,846,981 | 1,663,639 | 99.75 | 135.5 | Yes |
22 | F51 | DU | Fukui | 5,849,012 | 5,816,015 | 1,503,522 | 90.15 | 276.7 | No |
23 | F52 | DU | Fukui | 4,431,904 | 4,412,519 | 1,531,591 | 91.83 | 310.2 | Yes |
24 | F57 | GC | Fukui | 6,401,956 | 6,362,361 | 1,526,712 | 91.54 | 405.4 | Yes |
25 | F65 | CG | Fukui | 4,248,748 | 4,202,979 | 1,664,897 | 99.82 | 164.9 | Yes |
26 | F75 | GU | Fukui | 5,186,826 | 5,148,984 | 1,528,778 | 91.66 | 330.2 | Yes |
27 | F79 | GU | Fukui | 3,036,516 | 3,036,231 | 1,521,709 | 91.24 | 185.2 | Yes |
28 | F94 | GU | Fukui | 3,267,624 | 3,247,625 | 1,512,244 | 90.67 | 220.0 | Yes |
29 | F214 | GU | Fukui | 5,329,874 | 5,285,297 | 1,533,936 | 91.97 | 341.5 | Yes |
30 | F215 | GU | Fukui | 4,441,566 | 4,411,519 | 1,535,097 | 92.04 | 293.0 | Yes |
31 | F229 | GU | Fukui | 4,130,184 | 4,105,896 | 1,514,484 | 90.80 | 281.8 | Yes |
32 | HZ2 | CG | Hang Zhou | 3,953,756 | 3,926,283 | 1,511,585 | 90.63 | 261.8 | Yes |
33 | HZ11 | CG | Hang Zhou | 5,990,624 | 5,972,745 | 1,517,201 | 90.97 | 422.0 | Yes |
34 | HZ21 | GC | Hang Zhou | 6,697,176 | 6,676,385 | 1,530,926 | 91.79 | 406.4 | Yes |
35 | HZ34 | CG | Hang Zhou | 6,245,816 | 6,203,622 | 1,547,241 | 92.77 | 374.0 | Yes |
36 | HZ53 | DU | Hang Zhou | 6,631,022 | 6,593,830 | 1,556,114 | 93.30 | 402.0 | Yes |
37 | HZ67 | GC | Hang Zhou | 3,398,652 | 3,388,149 | 1,526,962 | 91.55 | 245.5 | Yes |
38 | HZ82 | CG | Hang Zhou | 3,984,240 | 3,968,256 | 1,532,373 | 91.88 | 276.1 | Yes |
39 | VN8 | GC | Ho Chi Minh | 5,876,658 | 5,850,475 | 1,537,665 | 92.19 | 403.1 | Yes |
40 | VN17 | GC | Ho Chi Minh | 6,810,950 | 6,786,447 | 1,520,811 | 91.18 | 465.3 | Yes |
41 | VN19 | GC | Ho Chi Minh | 4,071,510 | 4,060,588 | 1,521,512 | 91.23 | 284.2 | Yes |
42 | VN24 | GC | Ho Chi Minh | 4,241,646 | 4,226,765 | 1,533,944 | 91.97 | 294.1 | Yes |
43 | VN27 | GC | Ho Chi Minh | 4,315,490 | 4,298,304 | 1,547,804 | 92.80 | 283.4 | Yes |