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 = 1391494NA (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 = 19727510 (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