Table 1.
Summary results assembly, annotation and mapping
| Name in the study | True name, country of infection, year of isolation | Sample run accession | Sample accession | De novo assembly genomic size | Contigs number | Average Contigs Length | N50 | CDS detected | Reference used for mapping | Number of SNPs detected | % of reference mapped |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Ss_53G | Korea, 2000 | ERS387232 | ERR477376 | 4,698,814 | 402 | 11,688.59 | 29,856 | 4,495 | Ss 53G | 2 | 92.86 |
| Ss_53G_p | Korea, 2000 | ERS387243 | ERR477387 | 4,832,559 | 406 | 11,902.85 | 28,177 | 4,655 | Ss 53G | 2 | 92.80 |
| Ss_25931 | Unknown | ERS387235 | ERR477379 | 4,799,852 | 426 | 11,267.26 | 27,765 | 4,578 | Ss 53G | 630 | 89.51 |
| Sf 1a_Sh07.3008 | Sh07-3008, Cameroon, 2007 | ERS445026 | ERR573382 | 4,139,080 | 265 | 15,619.17 | 34,771 | 4,044 | Sf 2a 2457T | 3,459 | 86.58 |
| Sf 1b_Sh04.7434 | Sh04-7432, Tunisia, 2004 | ERS445024 | ERR573380 | 4,402,078 | 314 | 14,019.36 | 34,552 | 4,342 | Sf 2a 2457T | 2,935 | 87.63 |
| Sf 1b_Sh04.9462 | Sh04-9462, Cameroon, 2004 | ERS445025 | ERR573381 | 4,272,358 | 280 | 15,258.42 | 34,756 | 4,206 | Sf 2a 2457T | 3,207 | 87.36 |
| Sf 2a_2457T | Japan, 1954 | ERS387233 | ERR477377 | 4,681,429 | 344 | 13,608.81 | 35,441 | 4,583 | Sf 2a 2457T | 195 | 93.72 |
| Sf 2a_2457T_p | Japan, 1954 | ERS387242 | ERR477386 | 4,697,211 | 343 | 13,694.49 | 35,151 | 4,605 | Sf 2a 2457T | 192 | 93.88 |
| Sf 3a_6865_1 | Unknown | ERS387236 | ERR477380 | 4,665,099 | 335 | 13,925.67 | 35,495 | 4,550 | Sf 2a 2457T | 7,543 | 86.79 |
| Sf 3a_6865_2 | Unknown | ERS445023 | ERR573379 | 4,704,030 | 330 | 14,254.64 | 35,991 | 4,580 | Sf 2a 2457T | 7,708 | 87.08 |
| Sf 5a_M90T | Unknown <1980 | ERS387234 | ERR477378 | 4,486,899 | 327 | 13,721.40 | 32,160 | 4,391 | Sf 5a M90T | 25 | 97.82 |
| Sf 6_Sh10.5302_1 | 201005302, Madagascar, 2010 | ERS387237 | ERR477381 | 4,414,146 | 446 | 9,897.19 | 22,838 | 4,269 | Sb Sb227 | 4,408 | 89.30 |
| Sf 6_Sh10.5302_2 | 201005302, Madagascar, 2010 | ERS445029 | ERR573385 | 4,351,336 | 426 | 10,214.4 | 22,774 | 4,168 | Sb Sb227 | 4,406 | 89.10 |
| Sf 6_Sh10.3933 | 201003933, Nigeria, 2010 | ERS387238 | ERR477382 | 4,508,368 | 433 | 10,411.94 | 23,090 | 4,386 | Sb Sb227 | 4,456 | 89.33 |
| Sf 6_Sh10.8537 | 201008537, Egypt, 2010 | ERS387239 | ERR477383 | 4,524,547 | 425 | 10,645.99 | 23,238 | 4,398 | Sb Sb227 | 4,451 | 89.77 |
| Sf 6_Sh10.6306 | 201006306, India, 2010 | ERS387240 | ERR477384 | 4,481,178 | 439 | 10,207.69 | 23,066 | 4,367 | Sb Sb227 | 4,467 | 89.44 |
| Sf 6_Sh10.6237 | 201006237, Mexico, 2010 | ERS387241 | ERR477385 | 4,528,968 | 434 | 10,435.41 | 24,012 | 4,397 | Sb Sb227 | 4,389 | 89.39 |
| Sf 6_NCDC.2924-71 | NCDC 2924-71, Unknown, 1971 | ERS445027 | ERR573383 | 4,392,208 | 413 | 10,634.89 | 22,784 | 4,246 | Sb Sb227 | 4,288 | 89.66 |
| Sf 6_Sc544 | Unknown, <1977 | ERS445028 | ERR573384 | 4,430,667 | 415 | 10,676.31 | 22,494 | 4,302 | Sb Sb227 | 4,296 | 88.82 |
| Sf 6_Sh11.10088 | 201110088, France (Reunion Island), 2011 | ERS445030 | ERR573386 | 4,547,256 | 423 | 10,750.01 | 23,991 | 4,428 | Sb Sb227 | 4,483 | 89.88 |