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 49,765 C→T intergenic (+134/‑58) kefC → / → folA glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
RA 50,102 A→C I94L (ATT→CTT)  folA → type 3 dihydrofolate reductase
RA 1,858,499 G→C W131C (TGG→TGC)  yeaD → D‑hexose‑6‑phosphate mutarotase
RA 2,013,868 A→G N101D (AAC→GAC)  fliM → flagellar motor switch protein FliM
RA 2,236,491 A→C F214C (TTT→TGT)  folE ← GTP cyclohydrolase I FolE
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,370,587 G→T R65S (CGT→AGT)  sspA ← stringent starvation protein A
RA 4,171,725 G→C D185H (GAC→CAC)  rpoB → DNA‑directed RNA polymerase subunit beta

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356981 357577 597 2 [0] [1] 2 [lacA] [lacA]
* * ÷ NZ_CP009273 633098 633121 24 2 [1] [0] 2 ybdO/dsbG LysR family transcriptional regulator/thiol:disulfide interchange protein DsbG
* * ÷ NZ_CP009273 772340 772348 9 2 [0] [1] 2 tolA cell envelope integrity protein TolA
* * ÷ NZ_CP009273 950159 950212 54 2 [1] [1] 2 focA/ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 1061948 1061968 21 3 [1] [0] 2 agp bifunctional glucose‑1‑phosphatase/inositol phosphatase
* * ÷ NZ_CP009273 1165718 1165724 7 2 [0] [1] 2 ldtC L,D‑transpeptidase LdtC
* * ÷ NZ_CP009273 1193090 1193093 4 2 [1] [0] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1270274 1270286 13 2 [0] [1] 2 ychO inverse autotransporter invasin YchO
* * ÷ NZ_CP009273 1289634 1289645 12 3 [1] [1] 2 tdk/BW25113_RS06460 thymidine kinase/IS4 family transposase
* * ÷ NZ_CP009273 1314759 1314785 27 3 [1] [1] 2 trpD bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD
* * ÷ NZ_CP009273 1315169 1315182 14 3 [0] [1] 2 trpD bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD
* * ÷ NZ_CP009273 1362908 1362916 9 3 [1] [0] 2 pspA phage shock protein PspA
* * ÷ NZ_CP009273 1485796 1485805 10 2 [0] [1] 3 cybB/BW25113_RS07445 cytochrome b561/periplasmic protein
* * ÷ NZ_CP009273 1626760 1626767 8 2 [1] [1] 2 ydfJ/BW25113_RS25615 MHS family MFS transporter/hypothetical protein
* * ÷ NZ_CP009273 2580464 2580474 11 4 [0] [1] 2 narQ nitrate/nitrite two‑component system sensor histidine kinase NarQ
* * ÷ NZ_CP009273 3246145 3246162 18 2 [1] [0] 2 yhaH/yhaI DUF805 domain‑containing protein/DUF805 domain‑containing protein
* * ÷ NZ_CP009273 3629063 3629387 325 40 [0] [0] 2 [yhiM] [yhiM]
* * ÷ NZ_CP009273 3629549 3630241 693 2 [1] [1] 2 [yhiN] [yhiN]
* * ÷ NZ_CP009273 3630332 3630434 103 2 [1] [1] 2 yhiN NAD(P)/FAD‑dependent oxidoreductase
* * ÷ NZ_CP009273 3630517 3630653 137 2 [1] [0] 2 yhiN NAD(P)/FAD‑dependent oxidoreductase
* * ÷ NZ_CP009273 3630719 3631303 585 2 [0] [1] 2 [yhiN]–[pitA] [yhiN],[pitA]
* * ÷ NZ_CP009273 3631366 3631657 292 2 [1] [1] 2 pitA inorganic phosphate transporter PitA
* * ÷ NZ_CP009273 3631743 3632048 306 2 [1] [1] 2 pitA inorganic phosphate transporter PitA
* * ÷ NZ_CP009273 3632125 3632879 755 2 [1] [0] 2 [pitA]–[uspB] [pitA],[uspB]
* * ÷ NZ_CP009273 3632948 3633007 60 2 [0] [1] 2 uspB universal stress protein UspB
* * ÷ NZ_CP009273 3633074 3634017 944 2 [1] [0] 2 [uspB]–[BW25113_RS26230] [uspB],uspA,[BW25113_RS26225],[BW25113_RS26230]
* * ÷ NZ_CP009273 3634095 3635047 953 2 [0] [0] 2 [dtpB] [dtpB]
* * ÷ NZ_CP009273 3635091 3637267 2177 2 [0] [0] 2 [dtpB]–[prlC] [dtpB],rsmJ,[prlC]
* * ÷ NZ_CP009273 3637316 3638903 1588 2 [0] [1] 2 [prlC]–[rlmJ] [prlC],[rlmJ]
* * ÷ NZ_CP009273 3638913 3639964 1052 2 [1] [1] 2 [rlmJ]–[gorA] [rlmJ],[gorA]
* * ÷ NZ_CP009273 3640050 3640365 316 2 [1] [1] 2 gorA glutathione‑disulfide reductase
* * ÷ NZ_CP009273 3640407 3641029 623 2 [1] [1] 2 [gorA] [gorA]
* * ÷ NZ_CP009273 3641041 3641373 333 2 [1] [1] 2 dinQ dinQ
* * ÷ NZ_CP009273 3641384 3641533 150 2 [1] [0] 2 dinQ/arsR hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR
* * ÷ NZ_CP009273 3641572 3642452 881 2 [0] [0] 2 arsR–[arsB] arsR,[arsB]
* * ÷ NZ_CP009273 3642517 3642709 193 3 [1] [1] 2 arsB arsenite/antimonite:H(+) antiporter ArsB
* * ÷ NZ_CP009273 3642798 3642851 54 2 [1] [1] 2 arsB arsenite/antimonite:H(+) antiporter ArsB
* * ÷ NZ_CP009273 3642942 3643068 127 2 [1] [1] 2 arsB arsenite/antimonite:H(+) antiporter ArsB
* * ÷ NZ_CP009273 3643123 3643784 662 2 [1] [0] 2 [arsB]–[arsC] [arsB],[arsC]
* * ÷ NZ_CP009273 3643843 3644351 509 2 [0] [0] 2 [arsC] [arsC]
* * ÷ NZ_CP009273 3644399 3646527–3645396 998–2129 2 [0] [0] 4 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)16 (0.770) 11/166 0.5 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 = 120326116 (0.770)6 (0.360) 5/134 1.1 29.3% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 16 (0.960)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 1340634 =16 (0.770)4 (0.210) 3/154 1.7 24.4% coding (366/1986 nt) pdeR cyclic di‑GMP phosphodiesterase
?NZ_CP009273 1340740 = 10 (0.520)coding (260/1986 nt) pdeR cyclic di‑GMP phosphodiesterase
* ? NZ_CP009273 1972818 =0 (0.000)16 (0.770) 13/166 0.4 100% intergenic (‑364/‑416) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
?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 = 19728210 (0.000)5 (0.240) 5/166 1.4 100% intergenic (‑367/‑413) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
?NZ_CP009273 2095230 = NA (NA)pseudogene (1/354 nt) wbbL N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL
* ? NZ_CP009273 2282398 =NA (NA)40 (1.930) 21/166 0.1 100% pseudogene (3/2532 nt) yejO autotransporter YejO
?NZ_CP009273 = 3629062 0 (0.000)coding (862/1053 nt) yhiM DUF2776 domain‑containing protein
* ? NZ_CP009273 = 45325073 (0.140)14 (0.760) 12/148 0.4 65.6% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 12 (0.650)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA