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Table 1 Characteristics of clinical H. pylori isolates and sequencing results

From: Genetic variants of Helicobacter pylori type IV secretion system components CagL and CagI and their association with clinical outcomes

  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
  1. Okinawa is an island southwest of the main island of Japan. Kobe and Fukui are located on the main island of Japan. Hang Zhou is located in eastern China and Ho Chi Minh is in southern Vietnam. The 24 strains shown in italics were newly sequenced in this research
  2. CG chronic gastritis, GU gastric ulcer, DU duodenal ulcer, GC gastric cancer