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 49,791 G→A intergenic (+160/‑32) kefC → / → folA glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
MC JC 3,631,242 Δ66 bp coding (241‑306/1500 nt) pitA → inorganic phosphate transporter PitA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 153718 153738 21 2 [1] [1] 3 yadN/folK fimbrial protein/2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine diphosphokinase
* * ÷ NZ_CP009273 155825 155840 16 2 [0] [1] 3 gluQRS tRNA glutamyl‑Q(34) synthetase GluQRS
* * ÷ NZ_CP009273 212862 212905 44 2 [1] [1] 2 yaeF YaeF family permuted papain‑like enzyme
* * ÷ NZ_CP009273 235110 235129 20 3 [1] [1] 4 BW25113_RS01095 hypothetical protein
* * ÷ NZ_CP009273 356981 357571 591 2 [0] [1] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 572348 572439 92 2 [1] [1] 2 BW25113_RS02855/essD porin/phage lysis protein EssD
* * ÷ NZ_CP009273 578971 579033 63 2 [0] [1] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 633195 633207 13 2 [1] [0] 2 ybdO/dsbG LysR family transcriptional regulator/thiol:disulfide interchange protein DsbG
* * ÷ NZ_CP009273 656843 656883 41 2 [1] [1] 2 ybeF/lipB YbeF family transcriptional regulator/lipoyl(octanoyl) transferase LipB
* * ÷ NZ_CP009273 724403 724488 86 3 [1] [1] 2 kdpF/ybfA K(+)‑transporting ATPase subunit F/YbfA family protein
* * ÷ NZ_CP009273 748380 748391 12 2 [1] [0] 2 ybgD/gltA fimbrial protein/citrate synthase
* * ÷ NZ_CP009273 766392 766398 7 2 [0] [1] 2 mngB/cydA mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I
* * ÷ NZ_CP009273 903008 903036 29 2 [1] [1] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 982856 982929 74 2 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 993145 993184 40 2 [0] [1] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 993824 993896 73 2 [0] [1] 2 [elfA] [elfA]
* * ÷ NZ_CP009273 1069136 1069166 31 2 [1] [0] 2 rutA pyrimidine utilization protein A
* * ÷ NZ_CP009273 1197090 1197109 20 2 [1] [1] 4 BW25113_RS23630 hypothetical protein
* * ÷ NZ_CP009273 1205784 1205833 50 2 [1] [1] 2 [mcrA] [mcrA]
* * ÷ NZ_CP009273 1208168 1208225 58 2 [1] [1] 2 ycgX DUF1398 domain‑containing protein
* * ÷ NZ_CP009273 1225866 1225892 27 2 [0] [1] 2 hlyE/umuD hemolysin HlyE/translesion error‑prone DNA polymerase V autoproteolytic subunit
* * ÷ NZ_CP009273 1252993 1253008 16 2 [1] [1] 3 ychF redox‑regulated ATPase YchF
* * ÷ NZ_CP009273 1298626 1298641 16 4 [1] [1] 2 oppC oligopeptide ABC transporter permease OppC
* * ÷ NZ_CP009273 1317704 1317715 12 2 [1] [0] 2 yciV RNase AM
* * ÷ NZ_CP009273 1337186 1337221 36 4 [1] [1] 3 yciH stress response translation initiation inhibitor YciH
* * ÷ NZ_CP009273 1347820 1347830 11 3 [0] [0] 2 sapD peptide ABC transporter ATP‑binding protein SapD
* * ÷ NZ_CP009273 1363722 1363754 33 2 [1] [0] 2 pspD phage shock protein PspD
* * ÷ NZ_CP009273 1381495 1381510 16 3 [0] [1] 2 tyrR transcriptional regulator TyrR
* * ÷ NZ_CP009273 1392513 1392529 17 2 [1] [1] 4 uspE universal stress protein UspE
* * ÷ NZ_CP009273 1400088 1400108 21 2 [1] [1] 2 abgR/smrA LysR family transcriptional regulator/DNA endonuclease SmrA
* * ÷ NZ_CP009273 1415767 1415776 10 2 [1] [1] 3 ydaU YdaU family protein
* * ÷ NZ_CP009273 1416494 1416529 36 2 [0] [1] 2 ydaV ATP‑binding protein
* * ÷ NZ_CP009273 1459362 1459480 119 2 [1] [1] 2 [BW25113_RS25580] [BW25113_RS25580]
* * ÷ NZ_CP009273 1491681 1491684 4 2 [0] [0] 2 opgD glucan biosynthesis protein OpgD
* * ÷ NZ_CP009273 1537557 1537577 21 3 [1] [1] 3 narU nitrate/nitrite transporter NarU
* * ÷ NZ_CP009273 1540314 1540365 52 2 [1] [1] 2 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1573640 1573696 57 2 [0] [1] 4 yddA/BW25113_RS25610 ABC transporter ATP‑binding protein/permease/protein YneP
* * ÷ NZ_CP009273 1576775 1576813 39 3 [0] [1] 2 [ydeN] [ydeN]
* * ÷ NZ_CP009273 1635206 1635253 48 2 [1] [1] 2 [ynfU] [ynfU]
* * ÷ NZ_CP009273 1680512 1680650 139 2 [1] [1] 2 fumC class II fumarate hydratase
* * ÷ NZ_CP009273 1681688 1681709 22 2 [0] [1] 2 fumB class I fumarate hydratase
* * ÷ NZ_CP009273 1714008 1714018 11 2 [1] [0] 2 anmK/slyB anhydro‑N‑acetylmuramic acid kinase/outer membrane lipoprotein SlyB
* * ÷ NZ_CP009273 1720910 1720953 44 3 [0] [1] 2 [nemA] [nemA]
* * ÷ NZ_CP009273 1781395 1781397 3 2 [0] [0] 2 ppsA/ppsR phosphoenolpyruvate synthase/posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR
* * ÷ NZ_CP009273 1783765 1783875 111 2 [1] [1] 3 [hemP] [hemP]
* * ÷ NZ_CP009273 1807452 1807566 115 2 [0] [1] 2 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1812629 1812675 47 2 [1] [0] 2 celF 6‑phospho‑beta‑glucosidase
* * ÷ NZ_CP009273 1816597 1816618 22 3 [1] [1] 2 osmE/nadE osmotically‑inducible lipoprotein OsmE/ammonia‑dependent NAD(+) synthetase
* * ÷ NZ_CP009273 1884245 1884281 37 2 [0] [1] 3 yeaY Slp family lipoprotein YeaY
* * ÷ NZ_CP009273 1891605 1891633 29 2 [1] [1] 2 sdaA L‑serine ammonia‑lyase
* * ÷ NZ_CP009273 1907939 1907956 18 2 [1] [1] 2 prc carboxy terminal‑processing peptidase
* * ÷ NZ_CP009273 1980189 1980229 41 2 [0] [1] 2 araF/ftnB arabinose ABC transporter substrate‑binding protein AraF/non‑heme ferritin‑like protein
* * ÷ NZ_CP009273 1982110 1982125 16 2 [1] [0] 2 yecR/ftnA YecR‑like lipofamily protein/non‑heme ferritin
* * ÷ NZ_CP009273 1990357 1990395 39 2 [1] [0] 2 sdiA/yecC transcriptional regulator SdiA/L‑cystine ABC transporter ATP‑binding protein YecC
* * ÷ NZ_CP009273 2051020 2051076 57 4 [1] [1] 2 [yeeN] [yeeN]
* * ÷ NZ_CP009273 2051436 2051489 54 3 [1] [0] 3 yeeN/BW25113_RS10360 YebC/PmpR family DNA‑binding transcriptional regulator/tRNA‑Asn
* * ÷ NZ_CP009273 2052759 2052784 26 6 [1] [1] 2 yeeO toxic metabolite efflux MATE transporter YeeO
* * ÷ NZ_CP009273 2100179 2100202 24 2 [0] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2185786 2185876 91 2 [1] [1] 3 yehD/yehE fimbrial protein/YehE family protein
* * ÷ NZ_CP009273 2279600 2279623 24 2 [1] [1] 2 [yejM] [yejM]
* * ÷ NZ_CP009273 2380280 2380299 20 2 [1] [1] 3 yfbL M28 family metallopeptidase
* * ÷ NZ_CP009273 2463666 2463748 83 2 [1] [1] 3 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463862 2463868 7 2 [1] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2571510 2571549 40 2 [1] [1] 2 maeB NADP‑dependent oxaloacetate‑decarboxylating malate dehydrogenase
* * ÷ NZ_CP009273 2605245 2605270 26 2 [1] [1] 2 [hyfR] [hyfR]
* * ÷ NZ_CP009273 2623017 2623092 76 2 [1] [1] 4 yfgG/yfgH YfgG family protein/glycine zipper 2TM domain‑containing protein
* * ÷ NZ_CP009273 2898925 2898949 25 2 [1] [1] 2 BW25113_RS14445 hypothetical protein
* * ÷ NZ_CP009273 3262540 3262606 67 2 [1] [1] 2 yhaC YhaC family protein
* * ÷ NZ_CP009273 3798237 3798264 28 2 [0] [1] 2 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 4080292 4080343 52 2 [1] [1] 2 fdhD/yiiG formate dehydrogenase accessory sulfurtransferase FdhD/YiiG family protein
* * ÷ NZ_CP009273 4240720 4240758 39 2 [1] [1] 2 BW25113_RS20970 SopA family protein
* * ÷ NZ_CP009273 4466666 4466719 54 2 [1] [1] 3 BW25113_RS22080 hypothetical protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)31 (2.020) 22/166 0.0 58.5% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 22 (1.430)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 = 12032619 (0.590)9 (0.730) 8/134 0.4 63.7% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 3 (0.240)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 19727511 (0.070)13 (0.850) 10/166 0.4 92.9% 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 = 45325074 (0.260)7 (0.510) 4/148 1.0 57.0% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 7 (0.510)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA