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 49,912 G→T W30C (TGG→TGT)  folA → type 3 dihydrofolate reductase
RA 214,743 A→C Y174D (TAC→GAC)  proS ← proline‑‑tRNA ligase
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,754,231 G→T R127S (CGC→AGC)  selA ← L‑seryl‑tRNA(Sec) selenium transferase
RA 4,267,454 C→T R20C (CGC→TGC)  soxR → redox‑sensitive transcriptional activator SoxR

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356978 357585 608 2 [1] [0] 2 [lacA] [lacA]
* * ÷ NZ_CP009273 385397 385475 79 3 [1] [0] 2 hemB/BW25113_RS01915 porphobilinogen synthase/outer membrane autotransporter barrel domain‑containing protein
* * ÷ NZ_CP009273 428530 428558 29 2 [1] [1] 2 nrdR transcriptional regulator NrdR
* * ÷ NZ_CP009273 463327 463336 10 2 [0] [1] 2 cof HMP‑PP phosphatase
* * ÷ NZ_CP009273 489033 489047 15 2 [1] [1] 2 dnaX DNA polymerase III subunit gamma/tau
* * ÷ NZ_CP009273 518572 518587 16 2 [0] [1] 3 ybbP/rhsD ABC transporter permease/rhs element protein RhsD
* * ÷ NZ_CP009273 578747 578775 29 2 [1] [0] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 612270 612298 29 2 [1] [1] 3 entF enterobactin non‑ribosomal peptide synthetase EntF
* * ÷ NZ_CP009273 616040 616050 11 4 [1] [1] 5 fepG iron‑enterobactin ABC transporter permease
* * ÷ NZ_CP009273 647503 647546 44 2 [1] [0] 2 citC/dpiB [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
* * ÷ NZ_CP009273 716347 716425 79 2 [1] [1] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 718948 719079 132 2 [1] [1] 3 kdpD two‑component system sensor histidine kinase KdpD
* * ÷ NZ_CP009273 729584 729593 10 2 [0] [1] 3 BW25113_RS03630/BW25113_RS03635 hypothetical protein/RHS repeat protein
* * ÷ NZ_CP009273 741901 741929 29 2 [1] [1] 2 nei endonuclease VIII
* * ÷ NZ_CP009273 786099 786129 31 2 [1] [1] 2 galT galactose‑1‑phosphate uridylyltransferase
* * ÷ NZ_CP009273 799224 799315 92 2 [0] [1] 3 ybhJ hydratase
* * ÷ NZ_CP009273 830602 830679 78 2 [1] [1] 2 [dinG] [dinG]
* * ÷ NZ_CP009273 903021 903034 14 2 [1] [1] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 906405 906426 22 3 [1] [1] 2 poxB ubiquinone‑dependent pyruvate dehydrogenase
* * ÷ NZ_CP009273 950175 950209 35 2 [0] [1] 5 focA/ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 988436 988479 44 2 [1] [1] 2 pepN aminopeptidase N
* * ÷ NZ_CP009273 1105819 1105825 7 2 [0] [0] 2 mdoG glucans biosynthesis protein MdoG
* * ÷ NZ_CP009273 1144762 1144777 16 3 [0] [1] 2 fabH beta‑ketoacyl‑ACP synthase III
* * ÷ NZ_CP009273 1164381 1164441 61 2 [1] [1] 3 comR/bhsA TetR family copper‑responsive transcriptional repressor ComR/multiple stress resistance protein BhsA
* * ÷ NZ_CP009273 1172345 1172358 14 2 [0] [1] 2 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1188148 1188158 11 3 [1] [0] 3 mnmA tRNA 2‑thiouridine(34) synthase MnmA
* * ÷ NZ_CP009273 1191295 1191307 13 2 [0] [0] 2 icd NADP‑dependent isocitrate dehydrogenase
* * ÷ NZ_CP009273 1193086 1193156 71 2 [1] [1] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1207528 1207608 81 4 [1] [1] 2 iraM/BW25113_RS25985 anti‑adapter protein IraM/protein YmgK
* * ÷ NZ_CP009273 1213756 1213773 18 2 [1] [1] 2 pdeG cyclic diguanylate phosphodiesterase
* * ÷ NZ_CP009273 1305549 1305559 11 2 [0] [1] 3 tonB TonB system transport protein TonB
* * ÷ NZ_CP009273 1314776 1314830 55 3 [1] [1] 2 trpD bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD
* * ÷ NZ_CP009273 1327981 1327989 9 4 [1] [0] 3 topA/cysB type I DNA topoisomerase/HTH‑type transcriptional regulator CysB
* * ÷ NZ_CP009273 1424262 1424396 135 2 [1] [1] 2 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1424445 1424490 46 2 [1] [1] 2 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1451677 1451709 33 2 [1] [1] 2 paaK phenylacetate‑CoA oxygenase/reductase subunit PaaK
* * ÷ NZ_CP009273 1459374 1459506 133 2 [0] [1] 2 BW25113_RS25580 BW25113_RS25580
* * ÷ NZ_CP009273 1519265 1519308 44 2 [1] [1] 2 ansP L‑asparagine permease
* * ÷ NZ_CP009273 1576903 1576989 87 2 [0] [1] 3 ydeN/ydeO sulfatase/acid stress response transcriptional regulator YdeO
* * ÷ NZ_CP009273 1580904 1580932 29 2 [1] [1] 2 ydeP/ydeQ acid resistance putative oxidoreductase YdeP/fimbrial protein
* * ÷ NZ_CP009273 1627111 1627117 7 2 [1] [1] 2 ydfJ/BW25113_RS25615 MHS family MFS transporter/hypothetical protein
* * ÷ NZ_CP009273 1663752 1663827 76 2 [1] [0] 3 ynfL LysR family transcriptional regulator
* * ÷ NZ_CP009273 1674459 1674469 11 3 [0] [1] 3 ydgI amino acid permease
* * ÷ NZ_CP009273 1749026 1749088 63 2 [0] [1] 2 ydhY/fumD ferredoxin‑like protein/fumarate hydratase FumD
* * ÷ NZ_CP009273 1770922 1770953 32 2 [1] [0] 2 ydiF acyl CoA:acetate/3‑ketoacid CoA transferase
* * ÷ NZ_CP009273 1800517 1800551 35 3 [1] [1] 2 ydiY/pfkB YdiY family protein/6‑phosphofructokinase II
* * ÷ NZ_CP009273 1925028 1925038 11 3 [1] [0] 3 yebG/purT DNA damage‑inducible protein YebG/formate‑dependent phosphoribosylglycinamide formyltransferase
* * ÷ NZ_CP009273 1952572 1952596 25 2 [1] [1] 2 torY/cutC NapC/NirT family cytochrome c/copper homeostasis protein CutC
* * ÷ NZ_CP009273 1984654 1984659 6 2 [1] [0] 4 yecA UPF0149 family protein YecA
* * ÷ NZ_CP009273 2004835 2004897 63 2 [1] [1] 2 BW25113_RS10120 DUF5503 domain‑containing protein
* * ÷ NZ_CP009273 2033042 2033113 72 2 [1] [1] 2 msrP protein‑methionine‑sulfoxide reductase catalytic subunit MsrP
* * ÷ NZ_CP009273 2096913 2097006 94 2 [0] [1] 4 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2266374 2266422 49 3 [1] [1] 2 yejA extracellular solute‑binding protein
* * ÷ NZ_CP009273 2270439 2270445 7 2 [1] [0] 3 yejF microcin C ABC transporter ATP‑binding protein YejF
* * ÷ NZ_CP009273 2337771 2337777 7 2 [1] [0] 2 yfaL/nrdA AIDA‑I family autotransporter adhesin YfaL/EhaC/ribonucleoside‑diphosphate reductase subunit alpha
* * ÷ NZ_CP009273 2367632 2367656 25 2 [1] [1] 2 menE o‑succinylbenzoate‑‑CoA ligase
* * ÷ NZ_CP009273 2491851 2491939 89 2 [0] [1] 3 alaC/ypdA alanine transaminase/two‑component system sensor histidine kinase YpdA
* * ÷ NZ_CP009273 2505243 2505275 33 4 [1] [1] 2 mntH Nramp family divalent metal transporter
* * ÷ NZ_CP009273 2534361 2534377 17 2 [0] [0] 2 cysW sulfate/thiosulfate ABC transporter permease CysW
* * ÷ NZ_CP009273 2686856 2686881 26 2 [1] [1] 2 purL phosphoribosylformylglycinamidine synthase
* * ÷ NZ_CP009273 2766774 2766806 33 2 [1] [1] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2768281 2768291 11 2 [1] [0] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2877656 2877670 15 2 [0] [1] 2 casA/cas3 type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3
* * ÷ NZ_CP009273 3280520 3280530 11 2 [0] [1] 5 agaI/yraH galactosamine‑6‑phosphate isomerase/fimbrial protein
* * ÷ NZ_CP009273 3354488 3354532 45 2 [1] [1] 2 gltD/gltF glutamate synthase subunit GltD/DUF1120 domain‑containing protein
* * ÷ NZ_CP009273 3626938 3628066 1129 21 [0] [0] 2 [BW25113_RS18065] [BW25113_RS18065]
* * ÷ NZ_CP009273 3628133 3628201 69 2 [0] [0] 2 [yhiM] [yhiM]
* * ÷ NZ_CP009273 3628278 3628979 702 2 [0] [0] 2 yhiM DUF2776 domain‑containing protein
* * ÷ NZ_CP009273 3629036 3632624 3589 2 [0] [0] 2 [yhiM]–pitA [yhiM],yhiN,pitA
* * ÷ NZ_CP009273 3632685 3638975 6291 2 [0] [1] 2 uspB–[rlmJ] uspB,uspA,BW25113_RS26225,BW25113_RS26230,dtpB,rsmJ,prlC,[rlmJ]
* * ÷ NZ_CP009273 3639001 3641416 2416 2 [1] [1] 2 [rlmJ]–dinQ [rlmJ],gorA,dinQ
* * ÷ NZ_CP009273 3641457 3643202 1746 2 [1] [0] 2 arsR–[arsB] arsR,[arsB]
* * ÷ NZ_CP009273 3643272 3646510–3645392 2121–3239 3 [1] [1] 2 [arsB]–[BW25113_RS18160] [arsB],arsC,BW25113_RS18155,[BW25113_RS18160]
* * ÷ NZ_CP009273 3790455 3790506 52 2 [1] [1] 2 waaL O‑antigen ligase
* * ÷ NZ_CP009273 3798059 3798086 28 2 [1] [0] 2 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 3969691 3969707 17 2 [1] [1] 4 wzxE lipid III flippase WzxE

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)38 (2.340) 27/170 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 =1 (0.060)12 (0.910) 9/138 0.3 93.0% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 1 (0.080)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 12032611 (0.060)17 (1.290) 15/138 0.1 94.9% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 1 (0.080)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 19727512 (0.120)33 (2.040) 18/170 0.1 94.3% 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 2282400 =NA (NA)21 (1.330) 14/166 0.2 100% pseudogene (1/2532 nt) yejO autotransporter YejO
?NZ_CP009273 = 3626937 0 (0.000)pseudogene (882/1607 nt) BW25113_RS18065 YhiJ/YhiL family protein
* ? NZ_CP009273 = 45325076 (0.370)4 (0.280) 3/152 1.3 29.2% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 14 (0.970)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA