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 169,686 Δ1 bp coding (2203/2244 nt) fhuA → ferrichrome outer membrane transporter
MC JC 257,908 Δ776 bp [crl] [crl]
RA 909,353 G→A A566V (GCG→GTG)  poxB ← pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding
JC JC 911,086 IS2 (–) +5 bp intergenic (‑37/+92) poxB ← / ← hcr pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent
RA 1,159,199 G→T G444V (GGC→GTC)  ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
JC JC 1,293,032 IS1 (–) +8 bp intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
RA 2,132,787 A→C I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,173,363 Δ2 bp intergenic (‑1/+1) gatC ← / ← gatC pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 3,560,455 +G intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
JC JC 3,801,411 IS5 (–) +4 bp coding (586‑589/1017 nt) waaR ← lipopolysaccharide 1,2‑glucosyltransferase; UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
MC JC 3,815,859 Δ82 bp [rph]–[rph] [rph], [rph]
JC 4,001,645 Δ5 bp coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,184,543 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 121719 121881 163 5 [4] [3] 6 aroP/pdhR aromatic amino acid transporter/pyruvate dehydrogenase complex repressor; autorepressor
* * ÷ NC_000913 123046 127537 4492 5 [3] [4] 5 [aceE]–[aceF] [aceE],[aceF]
* * ÷ NC_000913 152061 152201 141 5 [3] [4] 6 yadL putative fimbrial‑like adhesin protein
* * ÷ NC_000913 156285 156432 148 5 [4] [4] 6 [yadN] [yadN]
* * ÷ NC_000913 157101 157309 209 5 [3] [3] 6 [folK] [folK]
* * ÷ NC_000913 237162 237375 214 5 [4] [4] 5 [yafT] [yafT]
* * ÷ NC_000913 238197 238439 243 6 [4] [4] 5 [ykfM] [ykfM]
* * ÷ NC_000913 238565 238847 283 6 [4] [4] 5 [ykfM]–[yafU] [ykfM],[yafU]
* * ÷ NC_000913 313898 314055 158 5 [4] [4] 6 ykgP/eaeH pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified
* * ÷ NC_000913 390540 390713 174 6 [4] [4] 5 yaiT pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
* * ÷ NC_000913 570368 570506 139 5 [4] [4] 6 [ybcK] [ybcK]
* * ÷ NC_000913 583131 584027 897 5 [4] [4] 5 [tfaX]–[appY] [tfaX],[appY]
* * ÷ NC_000913 584408 584749 342 6 [4] [4] 6 [appY]–[ompT] [appY],[ompT]
* * ÷ NC_000913 585705 585849 145 5 [4] [4] 5 ompT/pauD DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER
* * ÷ NC_000913 656583 656650 68 5 [4] [3] 5 pagP phospholipid:lipid A palmitoyltransferase
* * ÷ NC_000913 661431 661600 170 6 [4] [4] 5 ybeF/lipB LysR family putative transcriptional regulator/octanoyltransferase; octanoyl‑[ACP]:protein N‑octanoyltransferase
* * ÷ NC_000913 736069 736348 280 5 [3] [4] 5 [ybfC] [ybfC]
* * ÷ NC_000913 770750 771221 472 5 [4] [4] 5 mngB/cydA alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
* * ÷ NC_000913 954476 954701 226 5 [3] [4] 5 focA/ycaO formate channel/ribosomal protein S12 methylthiotransferase accessory factor
* * ÷ NC_000913 1050833 1050951 119 5 [4] [3] 5 insB1/cspH IS1 transposase B/stress protein, member of the CspA‑family
* * ÷ NC_000913 1092892 1093032 141 5 [4] [4] 6 ycdT diguanylate cyclase, membrane‑anchored
* * ÷ NC_000913 1103258 1103622 365 5 [4] [4] 5 csgD/csgB csgBAC operon transcriptional regulator/curlin nucleator protein, minor subunit in curli complex
* * ÷ NC_000913 1211730 1212460 731 5 [3] [4] 6 [iraM] [iraM]
* * ÷ NC_000913 1216397 1216718 322 5 [4] [4] 5 [ariR] [ariR]
* * ÷ NC_000913 1223078 1223282 205 5 [4] [4] 6 [ymgI]–[ymgJ] [ymgI],[ymgJ]
* * ÷ NC_000913 1256067 1256339 273 5 [3] [4] 5 ycgV/ychF putative adhesin/catalase inhibitor protein; ATPase, K+‑dependent, ribosome‑associated
* * ÷ NC_000913 1299397 1300912 1516 5 [3] [4] 5 ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* * ÷ NC_000913 1527182 1527282 101 5 [3] [4] 5 yncH/rhsE IPR020099 family protein/pseudogene, Rhs family
* * ÷ NC_000913 1544999 1545533 535 5 [3] [4] 5 yddK pseudogene, leucine‑rich protein; putative glycoportein
* * ÷ NC_000913 1583873 1584126 254 6 [4] [3] 5 [safA] [safA]
* * ÷ NC_000913 1586556 1586640 85 5 [4] [3] 5 ydeP/ydeQ putative oxidoreductase/putative fimbrial‑like adhesin protein
* * ÷ NC_000913 1598159 1598592 434 5 [4] [3] 6 yneO/lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
* * ÷ NC_000913 1870301 1870484 184 5 [3] [4] 5 [yeaI] [yeaI]
* * ÷ NC_000913 1870546 1870775 230 5 [4] [4] 6 yeaI putative membrane‑anchored diguanylate cyclase
* * ÷ NC_000913 1907715 1907812 98 5 [4] [4] 6 yobF/yebO DUF2527 family heat‑induced protein/putative inner membrane protein
* * ÷ NC_000913 1979490 1979665 176 12 [0] [4] 5 insA/uspC IS1 repressor TnpA/universal stress protein
* * ÷ NC_000913 2012121 2012387 267 5 [4] [4] 5 [yedN] [yedN]
* * ÷ NC_000913 2033732 2034117 386 5 [4] [4] 5 [rseX]–[yedS] [rseX],[yedS]
* * ÷ NC_000913 2066306–2066464 2066569–2066466 3–264 5 [4] [3] 5 insH1 IS5 transposase and trans‑activator
* * ÷ NC_000913 2103253 2104240 988 5 [4] [4] 5 [wbbL]–[wbbK] [wbbL],[wbbK]
* * ÷ NC_000913 2104368 2104504 137 5 [3] [3] 5 wbbK lipopolysaccharide biosynthesis protein
* * ÷ NC_000913 2109078 2109564 487 5 [3] [4] 5 wzxB putative polisoprenol‑linked O‑antigen transporter
* * ÷ NC_000913 2383439 2383835 397 6 [4] [4] 5 elaD protease, capable of cleaving an AMC‑ubiquitin model substrate
* * ÷ NC_000913 2455733 2456131 399 5 [4] [4] 5 yfcV/sixA putative fimbrial‑like adhesin protein/phosphohistidine phosphatase
* * ÷ NC_000913 2469136 2469613 478 6 [4] [4] 5 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ NC_000913 2470146 2470507 362 5 [3] [4] 5 [gtrS] [gtrS]
* * ÷ NC_000913 2628952 2629130 179 5 [4] [4] 5 yfgF/yfgG cyclic‑di‑GMP phosphodiesterase, anaerobic/uncharacterized protein
* * ÷ NC_000913 2773593 2773915 323 5 [4] [4] 6 yfjW CP4‑57 prophage; putative inner membrane protein
* * ÷ NC_000913 2774131 2774237 107 5 [3] [4] 5 yfjW CP4‑57 prophage; putative inner membrane protein
* * ÷ NC_000913 2774338 2775029 692 5 [4] [3] 5 [yfjW] [yfjW]
* * ÷ NC_000913 2784173 2784443 271 5 [4] [4] 6 ypjC pseudogene
* * ÷ NC_000913 2784908 2785151 244 5 [4] [4] 5 [ypjC] [ypjC]
* * ÷ NC_000913 2785987 2786654 668 6 [4] [4] 5 [ygaQ] [ygaQ]
* * ÷ NC_000913 2788642 2788810 169 5 [4] [4] 5 [ygaQ] [ygaQ]
* * ÷ NC_000913 2903562 2903899 338 5 [4] [4] 5 ygcE/queE putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
* * ÷ NC_000913 2989687 2990113 427 5 [4] [3] 5 [yqeJ]–[yqeK] [yqeJ],yqeL,[yqeK]
* * ÷ NC_000913 2990120 2990532 413 5 [4] [3] 7 [yqeK] [yqeK]
* * ÷ NC_000913 2990832 2991111 280 5 [4] [4] 5 [ygeF]–ygeF [ygeF],ygeF
* * ÷ NC_000913 2992527 2992690 164 5 [4] [4] 5 ygeH putative transcriptional regulator
* * ÷ NC_000913 2993725 2993893 169 5 [4] [4] 6 [ygeI] [ygeI]
* * ÷ NC_000913 2994925 2995278 354 5 [4] [4] 5 [ygeK] [ygeK]
* * ÷ NC_000913 3006003 3006088 86 5 [3] [4] 5 ygeV/ygeW putative sigma‑54‑interacting transcriptional activator/putative carbamoyltransferase
* * ÷ NC_000913 3191950 3192106 157 5 [4] [4] 6 glgS/yqiJ motility and biofilm regulator/DUF1449 family inner membrane protein
* * ÷ NC_000913 3268912 3269375 464 6 [4] [4] 5 yhaC pentapetide repeats‑related protein
* * ÷ NC_000913 3362070 3362234 165 5 [4] [4] 5 [yhcA] [yhcA]
* * ÷ NC_000913 3423786–3424234 3424517–3424238 5–732 5 [4] [3] 5 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 3582093 3582440 348 5 [4] [4] 5 yhhZ putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
* * ÷ NC_000913 3582578 3582788 211 5 [4] [4] 5 yhhZ putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
* * ÷ NC_000913 3634354 3634746 393 6 [4] [4] 5 [yhiL] [yhiL]
* * ÷ NC_000913 3653847 3654028 182 5 [4] [4] 5 [slp] [slp]
* * ÷ NC_000913 3658574 3658697 124 5 [4] [4] 6 gadE gad regulon transcriptional activator
* * ÷ NC_000913 3664549 3664732 184 5 [4] [4] 5 [gadW] [gadW]
* * ÷ NC_000913 3768149 3768541 393 5 [4] [4] 5 [rhsJ]–[yibG] [rhsJ],[yibG]
* * ÷ NC_000913 3769550 3769754 205 5 [4] [4] 5 [yibV]–[yibV] [yibV],[yibV]
* * ÷ NC_000913 3769973 3770212 240 5 [4] [3] 5 [yibU]–yibU [yibU],yibU
* * ÷ NC_000913 3797000 3797377 378 5 [3] [4] 5 waaL O‑antigen ligase
* * ÷ NC_000913 3797696 3797841 146 5 [4] [4] 5 waaL O‑antigen ligase
* * ÷ NC_000913 3798070 3798478 409 6 [4] [4] 5 [waaL]–[waaU] [waaL],[waaU]
* * ÷ NC_000913 3798962 3799595 634 5 [4] [4] 5 [waaU]–[waaZ] [waaU],[waaZ]
* * ÷ NC_000913 3800250 3800484 235 6 [4] [4] 5 [waaY] [waaY]
* * ÷ NC_000913 3802739 3803079 341 5 [4] [4] 5 [waaO]–[waaB] [waaO],[waaB]
* * ÷ NC_000913 3804217 3805079 863 5 [4] [4] 5 waaS lipopolysaccharide rhamnose:KdoIII transferase; lipopolysaccharide core biosynthesis protein
* * ÷ NC_000913 3888374 3888489 116 5 [3] [4] 5 [tnaC] [tnaC]
* * ÷ NC_000913 4002535 4002727 193 5 [4] [4] 5 yigF DUF2628 family putative inner membrane protein
* * ÷ NC_000913 4063917 4064073 157 5 [4] [4] 5 ompL outer membrane porin L; putative sulpholipid porin
* * ÷ NC_000913 4250722 4250952 231 6 [4] [4] 5 [yjbI]–[yjbI] [yjbI],[yjbI]
* * ÷ NC_000913 4251597 4251981 385 5 [4] [3] 5 yjbI pseudogene, SopA‑related, pentapeptide repeats‑containing
* * ÷ NC_000913 4282299 4282571 273 6 [4] [4] 5 yjcF pentapeptide repeats protein
* * ÷ NC_000913 4476296 4476401 106 5 [3] [4] 6 yjgL SopA‑central‑domain‑like hexapeptide repeat protein
* * ÷ NC_000913 4476435 4476638 204 6 [4] [4] 5 yjgL SopA‑central‑domain‑like hexapeptide repeat protein
* * ÷ NC_000913 4476866 4477320 455 5 [3] [4] 6 [yjgL]–[argI] [yjgL],[argI]
* * ÷ NC_000913 4506320 4506494 175 5 [4] [4] 5 [yjhC]–[ythA] [yjhC],[ythA]
* * ÷ NC_000913 4540480 4540762 283 5 [4] [4] 5 nanC/fimB N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
* * ÷ NC_000913 4541591 4541951 361 5 [4] [3] 5 fimB/fimE tyrosine recombinase/inversion of on/off regulator of fimA/tyrosine recombinase/inversion of on/off regulator of fimA
* * ÷ NC_000913 4542673 4542792 120 5 [3] [3] 5 fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* * ÷ NC_000913 4572231 4572381 151 5 [4] [4] 5 yjiS/yjiT DUF1127 family protein/pseudogene

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =5 (0.130)12 (0.370) 12/232 1.3 64.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 9 (0.280)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12078055 (0.130)38 (1.170) 36/232 0.1 85.0% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 9 (0.280)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 19794890 (0.000)12 (0.320) 12/264 1.6 100% intergenic (‑274/‑264) insA/uspC IS1 repressor TnpA/universal stress protein
?NC_000913 = 2290113 NA (NA)noncoding (1/1195 nt) IS5 repeat region