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 1,613,576 A→C D67A (GAC→GCC)  marR → multiple antibiotic resistance transcriptional regulator MarR
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356951 357570 620 2 [1] [0] 2 [lacA] [lacA]
* * ÷ NZ_CP009273 716379 716413 35 2 [0] [0] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 1037683 1037716 34 3 [1] [1] 2 etk tyrosine‑protein kinase
* * ÷ NZ_CP009273 1172386 1172430 45 2 [0] [1] 2 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1282029 1282045 17 2 [1] [0] 3 narI/BW25113_RS23085 respiratory nitrate reductase subunit gamma/RtT sRNA
* * ÷ NZ_CP009273 1631986 1632008 23 2 [1] [0] 2 gnsB addiction module toxin, GnsA/GnsB family
* * ÷ NZ_CP009273 2189903 2189909 7 2 [0] [1] 4 metG/BW25113_RS25680 methionine‑‑tRNA ligase/WGR and DUF4132 domain‑containing protein
* * ÷ NZ_CP009273 2622466 2622495 30 2 [1] [1] 2 [BW25113_RS25940] [BW25113_RS25940]
* * ÷ NZ_CP009273 3629247 3629714 468 26 [0] [0] 2 [yhiM]–[yhiN] [yhiM],[yhiN]
* * ÷ NZ_CP009273 3629781 3630376 596 2 [0] [1] 2 yhiN NAD(P)/FAD‑dependent oxidoreductase
* * ÷ NZ_CP009273 3630403 3630531 129 2 [1] [0] 2 yhiN NAD(P)/FAD‑dependent oxidoreductase
* * ÷ NZ_CP009273 3630607 3631613 1007 2 [0] [1] 2 [yhiN]–[pitA] [yhiN],[pitA]
* * ÷ NZ_CP009273 3631616 3632789 1174 2 [1] [1] 2 [pitA]–[uspB] [pitA],[uspB]
* * ÷ NZ_CP009273 3632803 3632898 96 2 [1] [1] 2 uspB universal stress protein UspB
* * ÷ NZ_CP009273 3632989 3633268 280 2 [1] [1] 2 [uspB] [uspB]
* * ÷ NZ_CP009273 3633291 3634246 956 2 [1] [0] 2 uspA–[dtpB] uspA,BW25113_RS26225,BW25113_RS26230,[dtpB]
* * ÷ NZ_CP009273 3634337 3634487 151 3 [1] [1] 3 dtpB dipeptide/tripeptide permease DtpB
* * ÷ NZ_CP009273 3634573 3636588 2016 2 [0] [1] 2 [dtpB]–[prlC] [dtpB],rsmJ,[prlC]
* * ÷ NZ_CP009273 3636644 3637045 402 2 [1] [0] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637106 3637268 163 2 [0] [1] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637359 3637708 350 2 [1] [0] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3637769 3638564 796 2 [0] [0] 2 [prlC] [prlC]
* * ÷ NZ_CP009273 3638610 3639536 927 2 [0] [1] 2 [rlmJ] [rlmJ]
* * ÷ NZ_CP009273 3639654 3640017 364 2 [1] [1] 2 [gorA] [gorA]
* * ÷ NZ_CP009273 3640108 3640642 535 2 [1] [0] 2 gorA glutathione‑disulfide reductase
* * ÷ NZ_CP009273 3640706 3641958 1253 3 [1] [0] 2 [gorA]–[arsR] [gorA],dinQ,[arsR]
* * ÷ NZ_CP009273 3642001 3642530 530 2 [0] [1] 2 [arsR]–[arsB] [arsR],[arsB]
* * ÷ NZ_CP009273 3642538 3644731 2194 2 [1] [1] 2 [arsB]–[BW25113_RS18155] [arsB],arsC,[BW25113_RS18155]
* * ÷ NZ_CP009273 3644822 3645125 304 2 [1] [0] 2 BW25113_RS18155 hypothetical protein
* * ÷ NZ_CP009273 3645169 3646512–3645391 223–1344 2 [0] [1] 2 [BW25113_RS18155]–[BW25113_RS18160] [BW25113_RS18155],[BW25113_RS18160]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)54 (2.870) 27/168 0.0 NA intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 NA (NA)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 1203246 =0 (0.000)11 (0.730) 8/136 0.5 91.7% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 2 (0.130)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 12032610 (0.000)15 (0.990) 12/136 0.2 93.8% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 2 (0.130)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)14 (0.750) 10/166 0.5 78.0% intergenic (+145/‑128) BW25113_RS06980/ynaJ IS5‑like element IS5 family transposase/DUF2534 family protein
?NZ_CP009273 1972747 = 4 (0.210)intergenic (‑293/‑487) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* ? NZ_CP009273 = 19030724 (0.210)18 (0.960) 15/168 0.2 81.8% intergenic (‑49/‑110) mgrB/yobH PhoP/PhoQ regulator MgrB/YobH family protein
?NZ_CP009273 = 2096424 NA (NA)intergenic (‑68/+3) BW25113_RS10605/wbbL IS5‑like element IS5 family transposase/N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL
* ? NZ_CP009273 = 19727510 (0.000)20 (1.060) 14/168 0.3 100% 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)22 (1.170) 13/168 0.3 95.7% pseudogene (3/2532 nt) yejO autotransporter YejO
?NZ_CP009273 3512437 = 1 (0.050)intergenic (‑14/+387) aroK/hofQ shikimate kinase AroK/DNA uptake porin HofQ
* ? NZ_CP009273 = 2283591NA (NA)29 (1.560) 16/166 0.2 100% intergenic (‑67/‑388) BW25113_RS11435/narP IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP
?NZ_CP009273 = 3512441 0 (0.000)intergenic (‑18/+383) aroK/hofQ shikimate kinase AroK/DNA uptake porin HofQ
* ? NZ_CP009273 = 36292460 (0.000)25 (1.330) 18/168 0.1 100% coding (1046/1053 nt) yhiM DUF2776 domain‑containing protein
?NZ_CP009273 3645396 = NA (NA)pseudogene (746/747 nt) BW25113_RS18155 hypothetical protein
* ? NZ_CP009273 4532499 =2 (0.110)7 (0.420) 7/150 0.7 61.5% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 7 (0.420)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
* ? NZ_CP009273 = 45325072 (0.110)6 (0.360) 6/150 0.9 57.7% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 7 (0.420)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA