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Assembly_stats.rst

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ST131 Assembly Statistics of 157 Strains

Methodology

  1. Low-quality bases & read-pairs, together with Illumina adaptor sequences, were trimmed from the raw reads using Trimmomatic v0.36 (Bolger et al., 2014) (settings: LEADING:10 TRAILING:10 MINLEN:50 HEADCROP:10).
  2. The average sequence coverage depth was estimated from mapping reads to the complete chromosome of E. coli ST131 strain EC958 using SPANDx v3.2 (Sarovich & Price, 2014).
  3. Quality-trimmed paired-end reads were de novo assembled using the Microbial Genome Assembler Pipeline (MGAP).
MGAP implements:
  1. QUAST v4.5 (Gurevich et al., 2013) assessed the assembly statistics generated from MGAP by comparing each isolate to EC958.

Table. Quality control & assembly metrics for 142 Welsh isolates sequenced to coverage ≥20-fold:

Strain Estimated coverage (-fold) No. contigs ≥1kbp Total length (bp) GC (%) N50
BA16 40.7 88 5,297,485 50.80 225,953
BA42 120.8 64 5,269,659 50.69 268,007
BA43 35.2 63 5,236,807 50.69 226,190
BA44 59.6 66 5,203,917 50.74 234,062
BA47 78.1 67 5,271,594 50.69 235,977
BA68 87.4 39 5,197,813 50.61 360,017
BA70 48.0 52 5,175,026 50.76 426,957
BA108 85.6 59 5,228,742 50.73 375,014
BA115 57.0 60 5,252,089 50.66 225,814
BA116 46.1 62 5,137,252 50.80 225,914
BA130 72.8 57 4,995,114 50.73 272,278
BA133 80.2 71 5,290,074 50.66 224,811
BA155 33.0 79 5,364,310 50.61 222,489
BA156 96.3 65 5,317,485 50.76 379,052
BA164 40.7 61 5,066,840 50.69 221,693
BA166 68.2 50 5,152,183 50.79 316,585
BA167 50.8 78 5,269,782 50.70 230,427
BA176 27.7 72 5,260,991 50.77 224,289
BA177 88.3 63 5,253,232 50.69 234,398
BA178 52.5 51 5,152,555 50.75 276,193
BA187 58.1 76 5,262,949 50.69 228,314
BA203 58.8 59 5,189,327 50.76 249,934
BA210 66.8 60 5,265,740 50.75 191,296
BA264 31.3 81 5,324,397 50.66 185,396
BA306 33.3 64 5,019,437 50.72 354,032
BA307 59.2 72 5,145,503 50.71 203,341
BA337 76.5 53 5,082,765 50.79 499,502
BA352 81.2 68 5,213,560 50.78 212,265
BA377 50.3 70 5,308,726 50.69 282,618
BA389 80.6 79 5,293,796 50.62 236,197
BA392 60.0 54 5,193,784 50.74 411,196
BA394 63.2 91 5,248,955 50.59 174,506
BA397 53.4 71 5,088,782 50.79 222,638
BA408 59.5 70 5,267,864 50.69 320,063
BA412 84.8 67 5,286,319 50.73 227,535
BA417 43.0 47 5,161,880 50.69 369,769
BA418 95.3 56 5,235,387 50.80 199,587
BA434 120.6 61 5,257,449 50.70 236,650
BA435 64.6 60 5,202,902 50.84 320,127
BA437 103.2 73 5,249,371 50.71 279,150
BA440 52.0 73 5,385,925 50.66 212,854
BA445 79.9 82 5,428,585 50.66 246,504
BA446 91.6 66 5,293,370 50.78 194,929
BA461 121.4 52 5,016,793 50.72 380,654
BA464 108.5 82 5,304,798 50.68 269,078
BA487 61.5 83 5,011,352 50.71 292,786
BA490 114.5 92 5,356,585 50.70 218,672
BA494 79.1 86 5,252,933 50.68 378,887
BA496 90.5 47 5,119,322 50.74 365,000
BA497 60.5 68 5,267,488 50.69 344,882
BA515 71.6 63 5,260,506 50.69 231,546
BA517 91.9 63 5,267,804 50.69 231,364
BA523 67.7 69 5,119,854 50.71 293,747
BA575 37.7 36 5,084,062 50.73 329,326
BA655 68.1 68 5,089,797 50.66 224,226
BA669 68.0 45 5,187,105 50.81 277,022
BA694 29.1 341 5,154,547 50.92 28,518
BA730 22.0 380 5,114,774 51.09 23,071
BA810 38.5 233 5,168,786 50.87 39,344
BA829 25.1 364 5,054,941 51.01 23,620
BA871 29.4 312 5,148,625 50.90 30,061
BA876 25.3 378 5,175,205 50.98 23,411
BA901 31.2 261 5,038,995 50.72 34,848
BA909 30.3 275 5,157,958 50.92 33,840
BA910 32.8 276 5,211,662 50.88 34,907
BA942 25.6 313 4,778,961 50.92 26,138
BA1110 31.0 289 5,163,895 50.94 37,542
BA1112 21.8 373 5,133,034 50.88 26,288
BA1165 28.8 283 5,163,615 50.89 37,638
BA1243 13.5 897 4,747,308 51.27 7,502
BA1275 15.8 461 5,000,323 50.98 16,543
BA1279 12.9 668 4,958,370 51.00 10,998
BA1287 10.9 993 4,772,761 51.10 6,422
BA1293 29.9 260 5,334,146 50.85 43,134
BA1295 35.6 345 5,215,129 51.01 27,698
BA1344 13.5 523 4,987,869 50.94 14,544
BA1347 59.0 119 5,095,120 50.77 89,952
BA1353 45.3 66 5,110,261 50.72 192,060
BA1355 50.2 62 5,130,152 50.80 253,431
BA1368 61.5 79 5,281,069 50.68 229,569
BA1387 56.4 84 5,233,184 50.67 182,110
BA1390 47.7 100 5,080,851 50.66 221,214
BA1391 42.0 63 5,149,818 50.75 210,310
BA1393 52.4 79 5,015,343 50.67 349,741
BA1397 39.5 88 5,220,217 50.80 197,411
BA1404 48.2 90 5,279,705 50.67 157,134
BA1408 32.6 34 4,785,837 50.67 284,015
BA1413 49.7 127 5,290,467 50.61 238,152
BA1418 33.3 116 5,055,916 50.67 190,563
BA1422 32.1 110 5,262,004 50.71 142,864
BA1431 41.4 88 5,052,865 50.70 188,140
BA1435 39.9 108 5,476,377 50.66 159,076
BA1441 57.8 89 5,110,031 50.74 145,320
BA1442 43.4 94 5,209,293 50.49 156,584
BA1446 44.7 75 5,199,739 50.65 226,804
BA1447 49.5 102 5,303,113 50.67 173,701
BA1458 41.7 85 5,140,634 50.79 182,682
BA1482 32.5 77 5,077,900 50.69 203,840
BA1490 36.9 95 5,279,717 50.65 191,129
BA1496 45.5 98 5,254,168 50.76 162,946
BA1507 47.5 130 5,166,617 50.76 108,396
BA1509 31.7 65 5,094,575 50.61 262,514
BA1511 53.8 76 5,246,319 50.69 317,362
BA1512 38.0 82 5,213,355 50.68 192,513
BA1517 44.1 47 5,093,734 50.65 333,756
BA1542 39.2 140 5,472,702 50.72 169,994
BA1543 36.9 118 5,303,188 50.77 133,596
BA1553 24.7 97 5,396,040 50.68 186,201
BA1561 43.8 80 5,256,720 50.66 182,291
BA1570 32.4 61 5,096,028 50.73 242,888
BA1575 41.6 103 5,389,527 50.64 274,731
BA1581 41.5 89 5,383,614 50.59 229,543
BA1585 56.0 52 5,152,731 50.74 341,715
BA1588 61.4 167 5,212,376 50.65 88,958
BA1593 48.8 141 5,239,260 50.67 109,455
BA1606 52.1 58 5,073,770 50.78 311,341
BA1637 47.7 395 5,190,213 50.69 26,377
BA1688 56.6 180 5,091,922 50.68 84,605
BA1843 46.4 93 5,029,987 50.73 199,596
BA2000 52.5 158 5,246,115 50.69 123,898
BA2055 64.2 95 5,241,788 50.84 172,175
BA2056 58.8 100 5,071,449 50.71 139,739
BA2065 32.0 103 4,968,736 50.71 131,344
BA2075 88.8 115 5,331,739 50.71 163,065
BA2078 37.0 200 5,203,752 50.68 51,504
BA2079 45.2 115 5,124,900 50.70 81,753
BA2080 72.5 85 5,346,277 50.73 191,817
BA2081 48.6 386 4,993,499 50.80 23,688
BA2082 95.8 139 5,198,516 50.65 100,389
BA2088 41.5 209 5,155,144 50.89 51,890
BA2090 46.7 151 5,320,517 50.78 116,475
BA2091 36.2 272 5,306,670 50.83 53,526
BA2097 79.1 90 5,130,019 50.73 174,248
BA2098 93.8 150 4,805,145 50.72 78,155
BA2102 47.1 291 5,326,101 50.68 38,600
BA2105 51.9 89 5,062,533 50.63 234,016
BA2112 49.8 140 5,101,446 50.74 88,767
BA2113 38.0 356 5,306,832 50.94 36,104
BA2121 76.2 63 5,167,987 50.74 229,717
BA2123 53.6 164 5,141,008 50.55 86,260
BA2133 105.5 91 4,937,313 50.80 159,529
BA2134 52.3 219 5,159,253 50.73 76,686