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 49,884 C→A P21Q (CCG→CAG)  folA → type 3 dihydrofolate reductase
RA 1,858,499 G→C W131C (TGG→TGC)  yeaD → D‑hexose‑6‑phosphate mutarotase
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,390,244 T→C D304G (GAC→GGC)  rng ← ribonuclease G
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 233707 233760 54 3 [1] [1] 3 BW25113_RS01085/BW25113_RS01090 tRNA‑Asp/lipoprotein
* * ÷ NZ_CP009273 280866 280918 53 2 [1] [1] 2 [yagF] [yagF]
* * ÷ NZ_CP009273 356978 357569 592 2 [1] [1] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 380412 380427 16 4 [0] [1] 2 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 524148 524210 63 2 [0] [1] 2 BW25113_RS24960 hypothetical protein
* * ÷ NZ_CP009273 716403 716444 42 2 [0] [1] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 716499 716548 50 2 [1] [1] 2 [kdpE] [kdpE]
* * ÷ NZ_CP009273 748342 748415 74 2 [1] [1] 2 ybgD/gltA fimbrial protein/citrate synthase
* * ÷ NZ_CP009273 845156 845194 39 2 [1] [1] 3 rhtA threonine/homoserine exporter RhtA
* * ÷ NZ_CP009273 910083 910091 9 2 [0] [1] 3 lysO L‑lysine exporter LysO
* * ÷ NZ_CP009273 950184 950212 29 2 [0] [1] 2 focA/ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 968617 968646 30 2 [1] [1] 2 elyC envelope biogenesis factor ElyC
* * ÷ NZ_CP009273 974180 974204 25 2 [1] [0] 2 mukB chromosome partition protein MukB
* * ÷ NZ_CP009273 982810 982820 11 2 [1] [0] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 982913 982942 30 2 [0] [0] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 1037761 1037800 40 2 [1] [1] 2 etk tyrosine‑protein kinase
* * ÷ NZ_CP009273 1140709 1140709 1 2 [0] [0] 2 rluC 23S rRNA pseudouridine(955/2504/2580) synthase RluC
* * ÷ NZ_CP009273 1177213 1177245 33 2 [1] [1] 2 [potD] [potD]
* * ÷ NZ_CP009273 1181694 1181704 11 2 [1] [0] 2 pepT peptidase T
* * ÷ NZ_CP009273 1225849 1225927 79 2 [1] [0] 2 [hlyE] [hlyE]
* * ÷ NZ_CP009273 1307027 1307043 17 4 [1] [1] 2 yciB septation protein A
* * ÷ NZ_CP009273 1313016 1313025 10 2 [1] [1] 2 trpCF bifunctional indole‑3‑glycerol‑phosphate synthase TrpC/phosphoribosylanthranilate isomerase TrpF
* * ÷ NZ_CP009273 1341092 1341115 24 2 [1] [0] 2 BW25113_RS25050 hypothetical protein
* * ÷ NZ_CP009273 1350920 1350978 59 2 [1] [1] 2 sapA peptide ABC transporter substrate‑binding protein SapA
* * ÷ NZ_CP009273 1361791 1361818 28 3 [1] [1] 2 pspF phage shock protein operon transcriptional activator
* * ÷ NZ_CP009273 1424296 1424363 68 2 [1] [1] 2 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1459480 1459532 53 2 [0] [1] 2 [BW25113_RS25580] [BW25113_RS25580]
* * ÷ NZ_CP009273 1475217 1475224 8 2 [0] [1] 2 ynbD phosphatase PAP2/dual specificity phosphatase family protein
* * ÷ NZ_CP009273 1540441 1540556 116 2 [1] [1] 3 [yddG] [yddG]
* * ÷ NZ_CP009273 1575679 1575735 57 2 [1] [1] 2 ydeN sulfatase
* * ÷ NZ_CP009273 1576846 1576870 25 2 [1] [0] 3 ydeN/ydeO sulfatase/acid stress response transcriptional regulator YdeO
* * ÷ NZ_CP009273 1616373 1616377 5 2 [0] [1] 4 ydeE efflux MFS transporter YdeE
* * ÷ NZ_CP009273 1631784 1631892 109 2 [1] [1] 2 [gnsB] [gnsB]
* * ÷ NZ_CP009273 1646549 1646571 23 2 [1] [0] 2 BW25113_RS25635 tyrosine‑type recombinase/integrase
* * ÷ NZ_CP009273 1673748 1673761 14 2 [0] [1] 2 ydgH/ydgI DUF1471 family protein YdgH/amino acid permease
* * ÷ NZ_CP009273 1697064 1697078 15 2 [0] [1] 2 add adenosine deaminase
* * ÷ NZ_CP009273 1715500 1715523 24 2 [1] [1] 2 [ydhI]–[ydhJ] [ydhI],[ydhJ]
* * ÷ NZ_CP009273 1723611 1723619 9 2 [0] [1] 2 lhr ATP‑dependent helicase
* * ÷ NZ_CP009273 1800519 1800566 48 3 [1] [0] 3 ydiY/pfkB YdiY family protein/6‑phosphofructokinase II
* * ÷ NZ_CP009273 1807367 1807377 11 2 [0] [0] 2 BW25113_RS09050 hypothetical protein
* * ÷ NZ_CP009273 1807547 1807572 26 2 [1] [1] 2 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1888048 1888140 93 2 [1] [1] 2 yoaB/yoaC RidA family protein/DUF1889 family protein
* * ÷ NZ_CP009273 1954425 1954441 17 2 [0] [1] 2 argS arginine‑‑tRNA ligase
* * ÷ NZ_CP009273 2027311 2027421 111 3 [0] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2062030 2062068 39 2 [1] [1] 2 BW25113_RS10415/BW25113_RS24005 IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein
* * ÷ NZ_CP009273 2125488 2125503 16 2 [1] [0] 2 wcaC colanic acid biosynthesis glycosyltransferase WcaC
* * ÷ NZ_CP009273 2287847 2287850 4 3 [0] [1] 2 ccmF cytochrome c‑type biogenesis heme lyase CcmF
* * ÷ NZ_CP009273 2329049 2329049 1 2 [0] [0] 3 yfaA DUF2138 domain‑containing protein
* * ÷ NZ_CP009273 2377015 2377056 42 2 [1] [1] 2 elaD deubiquitinase ElaD
* * ÷ NZ_CP009273 2462937 2462949 13 2 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463656 2463727 72 3 [0] [1] 3 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2584434 2584506 73 2 [1] [1] 2 ypfM/yffB protein YpfM/ArsC family reductase
* * ÷ NZ_CP009273 2613692 2613702 11 2 [0] [1] 2 upp uracil phosphoribosyltransferase
* * ÷ NZ_CP009273 2622527 2622532 6 2 [1] [0] 2 BW25113_RS25940 hypothetical protein
* * ÷ NZ_CP009273 2662577 2662584 8 2 [1] [1] 2 hcaE aromatic ring‑hydroxylating dioxygenase subunit alpha
* * ÷ NZ_CP009273 2753695 2753744 50 2 [1] [0] 2 yfjI YfjI family protein
* * ÷ NZ_CP009273 3247145 3247167 23 2 [0] [1] 2 yhaJ DNA‑binding transcriptional regulator YhaJ
* * ÷ NZ_CP009273 3629063 3630224 1162 32 [0] [0] 2 [yhiM]–[yhiN] [yhiM],[yhiN]
* * ÷ NZ_CP009273 3630276 3633343 3068 2 [0] [1] 5 [yhiN]–uspB [yhiN],pitA,uspB
* * ÷ NZ_CP009273 3633429 3637313 3885 2 [1] [1] 2 uspA–[prlC] uspA,BW25113_RS26225,BW25113_RS26230,dtpB,rsmJ,[prlC]
* * ÷ NZ_CP009273 3637407 3637934 528 2 [1] [1] 2 prlC oligopeptidase A
* * ÷ NZ_CP009273 3638025 3642668 4644 2 [1] [1] 2 [prlC]–[arsB] [prlC],rlmJ,gorA,dinQ,arsR,[arsB]
* * ÷ NZ_CP009273 3642689 3646531–3645396 2708–3843 2 [1] [1] 2 [arsB]–BW25113_RS18160 [arsB],arsC,BW25113_RS18155,BW25113_RS18160
* * ÷ NZ_CP009273 4037432 4037474 43 2 [0] [0] 2 dsbA/yihF thiol:disulfide interchange protein DsbA/YdgA family protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)11 (0.730) 9/166 0.4 33.3% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 22 (1.450)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 2282398 =NA (NA)32 (2.110) 17/166 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 4532499 =0 (0.000)10 (0.740) 9/148 0.4 95.2% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 1 (0.070)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
* ? NZ_CP009273 = 45325070 (0.000)14 (1.040) 9/148 0.4 96.5% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 1 (0.070)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA