<table><tr><td>Flavobacterium johnsoniae</td><td>Coevolved</td><td>5</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>1</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>1</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>1</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>2</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>2</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>2</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>3</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>3</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>3</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>4</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>4</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>4</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>5</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>5</td></tr><tr><td>Flavobacterium johnsoniae</td><td>Monoculture evolved</td><td>5</td></tr><tr><td>Flavobacterium johnsoniae</td><td>tolc_33bp_recombinant</td><td>0</td></tr><tr><td>Flavobacterium johnsoniae</td><td>tolc_33bp_recombinant</td><td>0</td></tr><tr><td>Flavobacterium johnsoniae</td><td>tolc_33bp_recombinant</td><td>0</td></tr></table>
<table><thead><tr><th>File</th><th>% reads Q&gt;: reads</th><th>% mapped</th></tr></thead><tbody><tr><td>Burk_anc_S87_R1_001_paired</td><td>99.6</td><td>1782341</td><td>99.9</td></tr><tr><td>Burk_anc_S87_R1_001_unpaired</td><td>92.9</td><td>101358</td><td>99.8</td></tr><tr><td>Burk_anc_S87_R2_001_paired</td><td>99.1</td><td>1781191</td><td>95.4</td></tr><tr><td>Burk_coevo_R1_S93_R1_001_paired</td><td>99.6</td><td>1456068</td><td>99.9</td></tr><tr><td>Burk_coevo_R1_S93_R1_001_unpaired</td><td>93.7</td><td>113336</td><td>99.8</td></tr><tr><td>Burk_coevo_R1_S93_R2_001_paired</td><td>98.8</td><td>1454980</td><td>95.2</td></tr><tr><td>Burk_coevo_R2_S94_R1_001_paired</td><td>99.6</td><td>1171980</td><td>99.9</td></tr><tr><td>Burk_coevo_R2_S94_R1_001_unpaired</td><td>93.7</td><td>90937</td><td>99.8</td></tr><tr><td>Burk_coevo_R2_S94_R2_001_paired</td><td>98.8</td><td>1171047</td><td>95.6</td></tr><tr><td>Burk_coevo_R3_S95_R1_001_paired</td><td>99.6</td><td>1203099</td><td>99.9</td></tr><tr><td>Burk_coevo_R3_S95_R1_001_unpaired</td><td>94</td><td>100148</td><td>99.8</td></tr><tr><td>Burk_coevo_R3_S95_R2_001_paired</td><td>98.8</td><td>1201991</td><td>96.4</td></tr><tr><td>Burk_coevo_R4_S96_R1_001_paired</td><td>99.6</td><td>10181397</td><td>99.9</td></tr><tr><td>Burk_coevo_R4_S96_R1_001_unpaired</td><td>93.8</td><td>84656</td><td>99.8</td></tr><tr><td>Burk_coevo_R4_S96_R2_001_paired</td><td>98.8</td><td>1080524</td><td>94.2</td></tr><tr><td>Burk_coevo_R5_S97_R1_001_paired</td><td>99.6</td><td>1517293</td><td>99.9</td></tr><tr><td>Burk_coevo_R5_S97_R1_001_unpaired</td><td>93</td><td>102422</td><td>99.8</td></tr><tr><td>Burk_coevo_R5_S97_R2_001_paired</td><td>99</td><td>1516104</td><td>95.6</td></tr><tr><td>Burk_mono_R1_S88_R1_001_paired</td><td>99.6</td><td>1240546</td><td>99.9</td></tr><tr><td>Burk_mono_R1_S88_R1_001_unpaired</td><td>93.5</td><td>87509</td><td>99.8</td></tr><tr><td>Burk_mono_R1_S88_R2_001_paired</td><td>98.9</td><td>1239531</td><td>95.3</td></tr><tr><td>Burk_mono_R2_S89_R1_001_paired</td><td>99.6</td><td>1141925</td><td>99.3</td></tr><tr><td>Burk_mono_R2_S89_R1_001_unpaired</td><td>93.9</td><td>89352</td><td>99.5</td></tr><tr><td>Burk_mono_R2_S89_R2_001_paired</td><td>98.8</td><td>1140884</td><td>95.9</td></tr><tr><td>Burk_mono_R3_S90_R1_001_paired</td><td>99.6</td><td>1239128</td><td>99.9</td></tr><tr><td>Burk_mono_R3_S90_R1_001_unpaired</td><td>93.5</td><td>87335</td><td>99.8</td></tr><tr><td>Burk_mono_R3_S90_R2_001_paired</td><td>98.9</td><td>1238229</td><td>95.3</td></tr><tr><td>Burk_mono_R4_S91_R1_001_paired</td><td>99.6</td><td>1533822</td><td>99.9</td></tr><tr><td>Burk_mono_R4_S91_R1_001_unpaired</td><td>93.8</td><td>117734</td><td>99.8</td></tr><tr><td>Burk_mono_R4_S91_R2_001_paired</td><td>98.8</td><td>1532619</td><td>96.1</td></tr><tr><td>Burk_mono_R5_S92_R1_001_paired</td><td>99.6</td><td>1518053</td><td>99.9</td></tr><tr><td>Burk_mono_R5_S92_R1_001_unpaired</td><td>93.8</td><td>113007</td><td>99.8</td></tr><tr><td>Burk_mono_R5_S92_R2_001_paired</td><td>98.9</td><td>1516767</td><td>98</td></tr><tr><td>Fj_anc_S47_R1_001_paired</td><td>99.7</td><td>1086306</td><td>99.9</td></tr><tr><td>Fj_anc_S47_R1_001_unpaired</td><td>94.4</td><td>207587</td><td>99.7</td></tr><tr><td>Fj_anc_S47_R2_001_paired</td><td>99.1</td><td>1085767</td><td>99.9</td></tr><tr><td>Fj_co1_S48_R1_001_paired</td><td>99.8</td><td>844209</td><td>99.9</td></tr><tr><td>Fj_co1_S48_R1_001_unpaired</td><td>94.7</td><td>164471</td><td>99.8</td></tr><tr><td>Fj_co1_S48_R2_001_paired</td><td>99</td><td>843838</td><td>99.9</td></tr><tr><td>Fj_co2_S49_R1_001_paired</td><td>99.7</td><td>1187836</td><td>99.9</td></tr><tr><td>Fj_co2_S49_R1_001_unpaired</td><td>94.4</td><td>169960</td><td>99.7</td></tr><tr><td>Fj_co2_S49_R2_001_paired</td><td>99.3</td><td>1187195</td><td>99.9</td></tr><tr><td>Fj_co3_S50_R1_001_paired</td><td>99.7</td><td>989588</td><td>99.9</td></tr><tr><td>Fj_co3_S50_R1_001_unpaired</td><td>94.5</td><td>142475</td><td>99.8</td></tr><tr><td>Fj_co3_S50_R2_001_paired</td><td>99.3</td><td>989036</td><td>99.9</td></tr><tr><td>Fj_co4_S51_R1_001_paired</td><td>99.7</td><td>948034</td><td>99.9</td></tr><tr><td>Fj_co4_S51_R1_001_unpaired</td><td>94.1</td><td>136839</td><td>99.7</td></tr><tr><td>Fj_co4_S51_R2_001_paired</td><td>99.3</td><td>947580</td><td>99.9</td></tr><tr><td>Fj_co5_S52_R1_001_paired</td><td>99.5</td><td>864002</td><td>99.9</td></tr><tr><td>Fj_co5_S52_R1_001_unpaired</td><td>93.7</td><td>108985</td><td>99.6</td></tr></tbody></table>
<table><tr><td>Fj_co5_S52_R2_001_paired</td><td>99.2</td><td>863565</td><td>99.9</td></tr><tr><td>Fj_mc1_S53_R1_001_paired</td><td>99.6</td><td>930277</td><td>99.9</td></tr><tr><td>Fj_mc1_S53_R1_001_unpaired</td><td>93.8</td><td>115078</td><td>99.8</td></tr><tr><td>Fj_mc1_S53_R2_001_paired</td><td>99.3</td><td>929848</td><td>99.9</td></tr><tr><td>Fj_mc2_S54_R1_001_paired</td><td>99.7</td><td>1126329</td><td>99.9</td></tr><tr><td>Fj_mc2_S54_R1_001_unpaired</td><td>93.9</td><td>151560</td><td>99.7</td></tr><tr><td>Fj_mc2_S54_R2_001_paired</td><td>99.3</td><td>1125752</td><td>99.9</td></tr><tr><td>Fj_mc3_S55_R1_001_paired</td><td>99.7</td><td>1167708</td><td>99.9</td></tr><tr><td>Fj_mc3_S55_R1_001_unpaired</td><td>94.4</td><td>150160</td><td>99.7</td></tr><tr><td>Fj_mc3_S55_R2_001_paired</td><td>99.3</td><td>1167069</td><td>99.9</td></tr><tr><td>Fj_mc4_S56_R1_001_paired</td><td>99.7</td><td>611216</td><td>99.9</td></tr><tr><td>Fj_mc4_S56_R1_001_unpaired</td><td>94.4</td><td>87941</td><td>99.7</td></tr><tr><td>Fj_mc4_S56_R2_001_paired</td><td>99.3</td><td>610912</td><td>99.9</td></tr><tr><td>Fj_mc5_S57_R1_001_paired</td><td>99.7</td><td>648699</td><td>99.9</td></tr><tr><td>Fj_mc5_S57_R1_001_unpaired</td><td>94.2</td><td>82410</td><td>99.8</td></tr><tr><td>Fj_mc5_S57_R2_001_paired</td><td>99.4</td><td>648407</td><td>99.9</td></tr><tr><td>Flavo_33bp_eng_S98_R1_001_paired</td><td>99.7</td><td>1360293</td><td>100</td></tr><tr><td>Flavo_33bp_eng_S98_R1_001_unpaired</td><td>88.4</td><td>45693</td><td>99.9</td></tr><tr><td>Flavo_33bp_eng_S98_R2_001_paired</td><td>99.3</td><td>1359576</td><td>97.2</td></tr></table>
Coverage (replicon 1)

Coverage (replicon 2)

78.4 87.2

57 61

53.7 56.3

55.9 63.6

70.5 79.6

61.8 77.6

71.2 72.3

55 60.5

58.3 53.4

53.3 51.2

67.1 74.9

49.3

38.6

47.2

43.8

42.1
38.4

41.2

50.3

51.2

27.6

29.1

66.4