breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | |||||
---|---|---|---|---|---|
evidence | position | mutation | annotation | gene | description |
RA | 50,280 | T→C | F153S (TTT→TCT) | folA → | type 3 dihydrofolate reductase |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
RA | 4,267,806 | A→G | D137G (GAC→GGC) | soxR → | redox‑sensitive transcriptional activator SoxR |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 29228 | 29290 | 63 | 2 [1] | [1] 3 | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit |
* | * | ÷ | NZ_CP009273 | 356979 | 357567 | 589 | 2 [1] | [0] 2 | lacA | galactoside O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 396622 | 396647 | 26 | 4 [0] | [0] 2 | BW25113_RS25915 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 476545 | 476579 | 35 | 4 [1] | [1] 2 | tomB/acrB | Hha toxicity modulator TomB/efflux RND transporter permease AcrB |
* | * | ÷ | NZ_CP009273 | 578792 | 578804 | 13 | 2 [0] | [0] 3 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
* | * | ÷ | NZ_CP009273 | 716398 | 716474 | 77 | 2 [1] | [1] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 748292 | 748350 | 59 | 2 [1] | [1] 2 | ybgD/gltA | fimbrial protein/citrate synthase |
* | * | ÷ | NZ_CP009273 | 860584 | 860601 | 18 | 2 [1] | [1] 2 | [moeB]–[moeA] | [moeB],[moeA] |
* | * | ÷ | NZ_CP009273 | 982672 | 982690 | 19 | 2 [1] | [1] 2 | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
* | * | ÷ | NZ_CP009273 | 1098885 | 1098917 | 33 | 3 [1] | [1] 2 | csgD/csgB | biofilm master transcriptional regulator CsgD/curli minor subunit CsgB |
* | * | ÷ | NZ_CP009273 | 1148643 | 1148662 | 20 | 2 [1] | [0] 2 | fabF/pabC | beta‑ketoacyl‑ACP synthase II/aminodeoxychorismate lyase |
* | * | ÷ | NZ_CP009273 | 1193573 | 1193618 | 46 | 2 [1] | [0] 4 | BW25113_RS05920 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1205050 | 1205056 | 7 | 2 [1] | [0] 2 | BW25113_RS06005 | phage tail protein |
* | * | ÷ | NZ_CP009273 | 1225877 | 1225952 | 76 | 2 [1] | [1] 3 | hlyE/umuD | hemolysin HlyE/translesion error‑prone DNA polymerase V autoproteolytic subunit |
* | * | ÷ | NZ_CP009273 | 1242706 | 1242727 | 22 | 2 [1] | [0] 5 | treA | alpha,alpha‑trehalase |
* | * | ÷ | NZ_CP009273 | 1251757 | 1251762 | 6 | 2 [1] | [0] 2 | ycgV/ychF | autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF |
* | * | ÷ | NZ_CP009273 | 1267304 | 1267309 | 6 | 2 [1] | [1] 2 | [chaA] | [chaA] |
* | * | ÷ | NZ_CP009273 | 1267441 | 1267488 | 48 | 2 [1] | [1] 2 | chaA/chaB | sodium‑potassium/proton antiporter ChaA/putative cation transport regulator ChaB |
* | * | ÷ | NZ_CP009273 | 1373025 | 1373029 | 5 | 4 [1] | [0] 2 | ycjT | kojibiose phosphorylase |
* | * | ÷ | NZ_CP009273 | 1459415 | 1459428 | 14 | 2 [0] | [0] 2 | [BW25113_RS25580] | [BW25113_RS25580] |
* | * | ÷ | NZ_CP009273 | 1524272 | 1524314 | 43 | 2 [1] | [1] 2 | BW25113_RS07645/BW25113_RS26145 | RHS repeat protein/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1524495 | 1524598 | 104 | 2 [1] | [1] 2 | BW25113_RS26145 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1566576 | 1566600 | 25 | 2 [1] | [1] 2 | gadB/pqqL | glutamate decarboxylase/insulinase family protein |
* | * | ÷ | NZ_CP009273 | 1600909 | 1600926 | 18 | 2 [0] | [1] 2 | lsrF | 3‑hydroxy‑5‑phosphonooxypentane‑2,4‑dione thiolase |
* | * | ÷ | NZ_CP009273 | 1610143 | 1610153 | 11 | 2 [0] | [1] 2 | yneK | putative protein YneK |
* | * | ÷ | NZ_CP009273 | 1618836 | 1618882 | 47 | 2 [1] | [1] 2 | ydeI/ydeJ | YdeI family stress tolerance OB fold protein/2‑oxo‑tetronate isomerase |
* | * | ÷ | NZ_CP009273 | 1641055 | 1641067 | 13 | 3 [1] | [1] 3 | flxA/BW25113_RS23105 | FlxA‑like family protein/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1652272 | 1652316 | 45 | 3 [1] | [1] 2 | ynfD/ynfE | DUF1161 domain‑containing protein/dimethyl sulfoxide reductase subunit A |
* | * | ÷ | NZ_CP009273 | 1674378 | 1674388 | 11 | 5 [1] | [1] 2 | ydgI | amino acid permease |
* | * | ÷ | NZ_CP009273 | 1748982 | 1749057 | 76 | 2 [1] | [0] 2 | ydhY/fumD | ferredoxin‑like protein/fumarate hydratase FumD |
* | * | ÷ | NZ_CP009273 | 1764366 | 1764392 | 27 | 2 [1] | [1] 3 | ydiK | AI‑2E family transporter YdiK |
* | * | ÷ | NZ_CP009273 | 1902138 | 1902193 | 56 | 2 [1] | [1] 2 | yobF/yebO | DUF2627 domain‑containing protein/YebO family protein |
* | * | ÷ | NZ_CP009273 | 2027096 | 2027129 | 34 | 2 [1] | [1] 3 | drpB/ompC | cell division protein DrpB/porin OmpC |
* | * | ÷ | NZ_CP009273 | 2097005 | 2097028 | 24 | 2 [1] | [1] 3 | wbbK | glycosyltransferase family 1 protein |
* | * | ÷ | NZ_CP009273 | 2357862 | 2357916 | 55 | 2 [0] | [1] 3 | yfaZ/nudI | YfaZ family protein/nucleoside triphosphatase NudI |
* | * | ÷ | NZ_CP009273 | 2359231 | 2359248 | 18 | 3 [1] | [0] 2 | ais/arnB | lipopolysaccharide core heptose(II)‑phosphate phosphatase Ais/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
* | * | ÷ | NZ_CP009273 | 2379251 | 2379315 | 65 | 4 [1] | [1] 2 | yfbK/yfbL | VWA domain‑containing protein/M28 family metallopeptidase |
* | * | ÷ | NZ_CP009273 | 2449580 | 2449586 | 7 | 6 [0] | [0] 3 | yfcV/sixA | fimbrial protein/phosphohistidine phosphatase SixA |
* | * | ÷ | NZ_CP009273 | 2463656 | 2463694 | 39 | 2 [1] | [1] 2 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2505249 | 2505275 | 27 | 2 [1] | [0] 4 | mntH | Nramp family divalent metal transporter |
* | * | ÷ | NZ_CP009273 | 2520204 | 2520217 | 14 | 2 [1] | [0] 2 | [yfeR] | [yfeR] |
* | * | ÷ | NZ_CP009273 | 2613662 | 2613678 | 17 | 2 [1] | [1] 3 | upp | uracil phosphoribosyltransferase |
* | * | ÷ | NZ_CP009273 | 2779591 | 2779622 | 32 | 3 [1] | [1] 2 | BW25113_RS13825/BW25113_RS26005 | tRNA‑Ile/alpha‑amylase family glycosyl hydrolase |
* | * | ÷ | NZ_CP009273 | 2984530 | 2984595 | 66 | 2 [0] | [1] 3 | BW25113_RS14825/ygeG | hypothetical protein/tetratricopeptide repeat protein |
* | * | ÷ | NZ_CP009273 | 3246093 | 3246101 | 9 | 4 [0] | [0] 2 | yhaH/yhaI | DUF805 domain‑containing protein/DUF805 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 3463211 | 3463250 | 40 | 2 [1] | [1] 2 | [chiA] | [chiA] |
* | * | ÷ | NZ_CP009273 | 3629488 | 3633417 | 3930 | 25 [0] | [1] 3 | yhiN–uspB | yhiN,pitA,uspB |
* | * | ÷ | NZ_CP009273 | 3633476 | 3635247 | 1772 | 2 [0] | [1] 2 | [uspA]–[dtpB] | [uspA],BW25113_RS26225,BW25113_RS26230,[dtpB] |
* | * | ÷ | NZ_CP009273 | 3635324 | 3635587 | 264 | 2 [1] | [0] 2 | dtpB | dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3635676 | 3636015 | 340 | 2 [0] | [0] 2 | [dtpB]–[rsmJ] | [dtpB],[rsmJ] |
* | * | ÷ | NZ_CP009273 | 3636104 | 3638645 | 2542 | 2 [0] | [1] 2 | [rsmJ]–prlC | [rsmJ],prlC |
* | * | ÷ | NZ_CP009273 | 3638706 | 3641142 | 2437 | 2 [1] | [0] 2 | rlmJ–[dinQ] | rlmJ,gorA,[dinQ] |
* | * | ÷ | NZ_CP009273 | 3641220 | 3646512–3645398 | 4179–5293 | 2 [0] | [0] 2 | arsR–[BW25113_RS18160] | arsR,arsB,arsC,BW25113_RS18155,[BW25113_RS18160] |
* | * | ÷ | NZ_CP009273 | 3792682 | 3792712 | 31 | 2 [0] | [0] 2 | [waaZ] | [waaZ] |
* | * | ÷ | NZ_CP009273 | 4225606 | 4225637 | 32 | 2 [1] | [1] 2 | pgi/yjbE | glucose‑6‑phosphate isomerase/exopolysaccharide production protein YjbE |
* | * | ÷ | NZ_CP009273 | 4241742 | 4241751 | 10 | 2 [1] | [0] 4 | BW25113_RS20970 | SopA family protein |
* | * | ÷ | NZ_CP009273 | 4316740 | 4316768 | 29 | 3 [1] | [1] 2 | yjdM/crfC | zinc ribbon domain‑containing protein YjdM/clamp‑binding protein CrfC |
* | * | ÷ | NZ_CP009273 | 4562088 | 4562116 | 29 | 2 [0] | [1] 2 | yjiS/yjiT | DUF1127 domain‑containing protein/protein YjiT |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 15 (0.910) | 11/166 | 0.4 | 53.6% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
? | NZ_CP009273 | = 360286 | 13 (0.790) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
* | ? | NZ_CP009273 | 1203246 = | 7 (0.430) | 11 (0.830) | 8/134 | 0.4 | 74.2% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 2 (0.150) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 7 (0.430) | 5/164 | 1.1 | 100% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
? | NZ_CP009273 | 1972747 = | 0 (0.000) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
* | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 25 (1.520) | 15/166 | 0.2 | 100% | intergenic (‑297/‑483) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
? | NZ_CP009273 | = 2283592 | NA (NA) | intergenic (‑68/‑387) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP | |||||
* | ? | NZ_CP009273 | 2282398 = | NA (NA) | 24 (1.460) | 14/166 | 0.2 | 100% | pseudogene (3/2532 nt) | yejO | autotransporter YejO |
? | NZ_CP009273 | = 3629487 | 0 (0.000) | intergenic (+234/+81) | yhiM/yhiN | DUF2776 domain‑containing protein/NAD(P)/FAD‑dependent oxidoreductase | |||||
* | ? | NZ_CP009273 | 4532499 = | 2 (0.120) | 8 (0.540) | 8/148 | 0.5 | 57.6% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | 4532813 = | 10 (0.680) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |