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
RA 1,902,968 Δ1 bp coding (56/144 nt) mgrB ← PhoP/PhoQ regulator MgrB
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
JC 4,267,801 +CCG coding (405/465 nt) soxR → redox‑sensitive transcriptional activator SoxR
RA 4,458,295 T→G I285S (ATC→AGC)  mgtA → magnesium‑translocating P‑type ATPase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356968 357570 603 2 [1] [1] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 578972 579033 62 2 [1] [1] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 647607 647617 11 2 [1] [0] 2 citC/dpiB [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
* * ÷ NZ_CP009273 716379 716452 74 2 [1] [1] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 987880 987895 16 3 [0] [1] 3 pepN aminopeptidase N
* * ÷ NZ_CP009273 993134 993278 145 2 [1] [1] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1059485 1059495 11 2 [1] [1] 4 [yccE] [yccE]
* * ÷ NZ_CP009273 1192717 1192796 80 2 [1] [1] 2 ymfD class I SAM‑dependent methyltransferase
* * ÷ NZ_CP009273 1206620 1206671 52 4 [1] [0] 2 [mcrA] [mcrA]
* * ÷ NZ_CP009273 1207528 1207531 4 4 [0] [0] 2 iraM/BW25113_RS25985 anti‑adapter protein IraM/protein YmgK
* * ÷ NZ_CP009273 1380783 1380804 22 5 [0] [1] 2 ycjF YcjF family protein
* * ÷ NZ_CP009273 1380903 1380939 37 2 [1] [1] 4 ycjF/tyrR YcjF family protein/transcriptional regulator TyrR
* * ÷ NZ_CP009273 1389956 1390000 45 2 [1] [1] 2 ynaI low conductance mechanosensitive channel YnaI
* * ÷ NZ_CP009273 1459390 1459516 127 2 [1] [0] 2 BW25113_RS25580 BW25113_RS25580
* * ÷ NZ_CP009273 1485766 1485783 18 2 [0] [0] 2 cybB/BW25113_RS07445 cytochrome b561/periplasmic protein
* * ÷ NZ_CP009273 1521283 1521366 84 2 [0] [1] 2 yncH YncH family protein
* * ÷ NZ_CP009273 1521556 1521575 20 2 [1] [0] 3 yncH/BW25113_RS07645 YncH family protein/RHS repeat protein
* * ÷ NZ_CP009273 1581017 1581029 13 2 [0] [1] 3 ydeP/ydeQ acid resistance putative oxidoreductase YdeP/fimbrial protein
* * ÷ NZ_CP009273 1618523 1618540 18 5 [0] [1] 3 ydeI YdeI family stress tolerance OB fold protein
* * ÷ NZ_CP009273 1631426 1631462 37 2 [1] [0] 2 ydfO DUF1398 domain‑containing protein
* * ÷ NZ_CP009273 1632902 1632934 33 2 [0] [0] 4 [cspI] [cspI]
* * ÷ NZ_CP009273 1635220 1635285 66 8 [1] [1] 5 [ynfU] [ynfU]
* * ÷ NZ_CP009273 1750082 1750119 38 2 [1] [0] 2 pykF pyruvate kinase PykF
* * ÷ NZ_CP009273 1864867 1864870 4 2 [0] [0] 3 cdgI GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1896099 1896155 57 2 [1] [1] 3 yoaE/manX CNNM family cation transport protein YoaE/PTS mannose transporter subunit IIAB
* * ÷ NZ_CP009273 1912822 1912830 9 2 [0] [1] 3 yebT lipid‑binding membrane homeostasis protein YebT
* * ÷ NZ_CP009273 1980209 1980254 46 2 [1] [0] 2 araF/ftnB arabinose ABC transporter substrate‑binding protein AraF/non‑heme ferritin‑like protein
* * ÷ NZ_CP009273 2004882 2004902 21 2 [1] [0] 3 BW25113_RS10120 DUF5503 domain‑containing protein
* * ÷ NZ_CP009273 2008597 2008602 6 2 [0] [1] 3 fliG flagellar motor switch protein FliG
* * ÷ NZ_CP009273 2027317 2027372 56 2 [0] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2050211 2050277 67 2 [1] [1] 3 amn/yeeN AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator
* * ÷ NZ_CP009273 2246110 2246126 17 2 [1] [1] 4 yeiI sugar kinase
* * ÷ NZ_CP009273 2370758 2370816 59 2 [1] [1] 2 menH 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
* * ÷ NZ_CP009273 2462809 2462859 51 2 [0] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2462907 2462937 31 2 [0] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463057 2463069 13 2 [0] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2622497 2622540 44 2 [0] [1] 3 BW25113_RS25940 hypothetical protein
* * ÷ NZ_CP009273 2622952 2623015 64 3 [1] [1] 2 yfgG/yfgH YfgG family protein/glycine zipper 2TM domain‑containing protein
* * ÷ NZ_CP009273 2768272 2768289 18 2 [1] [1] 3 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2776935 2776949 15 3 [1] [1] 3 BW25113_RS24210/BW25113_RS25705 recombinase family protein/DUF5507 domain‑containing protein
* * ÷ NZ_CP009273 2897127 2897257 131 2 [1] [1] 2 ygcE/queE FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NZ_CP009273 2988539 2988660 122 3 [1] [1] 3 BW25113_RS14850/BW25113_RS26010 response regulator transcription factor/hypothetical protein
* * ÷ NZ_CP009273 3463343 3463398 56 2 [1] [1] 2 chiA/tuf bifunctional chitinase/lysozyme/elongation factor Tu
* * ÷ NZ_CP009273 3745315 3745334 20 2 [0] [1] 2 yiaT/yiaU MipA/OmpV family protein/LysR family transcriptional regulator
* * ÷ NZ_CP009273 3798414 3798447 34 2 [0] [0] 2 rfaS LPS core biosynthesis protein RfaS
* * ÷ NZ_CP009273 4080238 4080329 92 2 [1] [1] 2 fdhD/yiiG formate dehydrogenase accessory sulfurtransferase FdhD/YiiG family protein
* * ÷ NZ_CP009273 4531411 4531421 11 2 [1] [0] 2 fimB/fimE type 1 fimbria switch DNA invertase FimB/type 1 fimbria switch DNA invertase FimE

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)23 (1.390) 13/166 0.3 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 =10 (0.600)12 (0.900) 12/134 0.2 63.0% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 6 (0.450)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 120326110 (0.600)8 (0.600) 8/134 0.4 53.2% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 6 (0.450)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)8 (0.490) 6/164 0.9 100% intergenic (+145/‑128) BW25113_RS06980/ynaJ IS5‑like element IS5 family transposase/DUF2534 family protein
?NZ_CP009273 1972747 = 0 (0.000)intergenic (‑293/‑487) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* ? NZ_CP009273 = 19727511 (0.060)28 (1.690) 19/166 0.1 96.5% 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 2282398 =NA (NA)17 (1.020) 9/166 0.5 100% pseudogene (3/2532 nt) yejO autotransporter YejO
?NZ_CP009273 3512437 = 0 (0.000)intergenic (‑14/+387) aroK/hofQ shikimate kinase AroK/DNA uptake porin HofQ
* ? NZ_CP009273 = 2283591NA (NA)25 (1.530) 17/164 0.1 86.4% intergenic (‑67/‑388) BW25113_RS11435/narP IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP
?NZ_CP009273 = 3512441 4 (0.240)intergenic (‑18/+383) aroK/hofQ shikimate kinase AroK/DNA uptake porin HofQ