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 2,252,901 A→C intergenic (‑126/+297) psuK ← / ← fruA pseudouridine kinase/PTS fructose transporter subunit IIBC
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356976 357567 592 3 [0] [0] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 399056 399066 11 2 [1] [0] 2 [psiF] [psiF]
* * ÷ NZ_CP009273 468977 468988 12 3 [1] [1] 2 amtB ammonium transporter AmtB
* * ÷ NZ_CP009273 511662 511672 11 6 [1] [0] 2 fetA iron ABC transporter ATP‑binding protein FetA
* * ÷ NZ_CP009273 542543 542567 25 2 [1] [1] 2 fdrA acyl‑CoA synthetase FdrA
* * ÷ NZ_CP009273 567067 567097 31 2 [1] [1] 2 ybcM helix‑turn‑helix transcriptional regulator
* * ÷ NZ_CP009273 578897 578984 88 2 [1] [1] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 579257 579279 23 2 [1] [1] 2 appY DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 579472 579533 62 2 [0] [1] 3 appY DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 589642 589702 61 2 [1] [1] 2 cusS Cu(+)/Ag(+) sensor histidine kinase CusS
* * ÷ NZ_CP009273 613580 613589 10 2 [1] [1] 2 entF/wzz(fepE) enterobactin non‑ribosomal peptide synthetase EntF/LPS O‑antigen length regulator Wzz(fepE)
* * ÷ NZ_CP009273 617360 617406 47 2 [1] [1] 2 fepD Fe(3+)‑siderophore ABC transporter permease
* * ÷ NZ_CP009273 650721 650745 25 2 [1] [1] 2 dcuC anaerobic C4‑dicarboxylate transporter DcuC
* * ÷ NZ_CP009273 651704 651732 29 3 [1] [1] 3 dcuC/pagP anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP
* * ÷ NZ_CP009273 656868 656903 36 2 [1] [1] 2 ybeF/lipB YbeF family transcriptional regulator/lipoyl(octanoyl) transferase LipB
* * ÷ NZ_CP009273 701324 701359 36 3 [1] [1] 2 [nagE] [nagE]
* * ÷ NZ_CP009273 724884 724950 67 4 [0] [1] 3 ybfA/rhsC YbfA family protein/rhs element protein RhsC
* * ÷ NZ_CP009273 793084 793120 37 2 [0] [1] 2 ybhA bifunctional pyridoxal phosphate/fructose‑1,6‑bisphosphate phosphatase
* * ÷ NZ_CP009273 828591 828715 125 2 [1] [1] 2 dinG ATP‑dependent DNA helicase DinG
* * ÷ NZ_CP009273 829648 829668 21 2 [1] [1] 2 dinG ATP‑dependent DNA helicase DinG
* * ÷ NZ_CP009273 886671 886684 14 3 [1] [0] 2 nfsA nitroreductase NfsA
* * ÷ NZ_CP009273 912230 912242 13 4 [1] [1] 2 ybjD ATP‑dependent endonuclease
* * ÷ NZ_CP009273 955617 955701 85 2 [1] [1] 2 aroA/ycaL 3‑phosphoshikimate 1‑carboxyvinyltransferase/metallopeptidase YcaL
* * ÷ NZ_CP009273 969892 969949 58 2 [1] [0] 2 mukF chromosome partition protein MukF
* * ÷ NZ_CP009273 982923 982970 48 2 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 1012621 1012647 27 3 [1] [1] 2 ycbZ Lon protease family protein
* * ÷ NZ_CP009273 1028574 1028584 11 2 [1] [1] 2 hyaA hydrogenase 1 small subunit
* * ÷ NZ_CP009273 1051200 1051262 63 3 [0] [1] 2 torS TMAO reductase system sensor histidine kinase/response regulator TorS
* * ÷ NZ_CP009273 1054320 1054322 3 2 [0] [1] 2 torC pentaheme c‑type cytochrome TorC
* * ÷ NZ_CP009273 1075171 1075186 16 2 [0] [1] 2 putP sodium/proline symporter PutP
* * ÷ NZ_CP009273 1080325 1080348 24 2 [1] [1] 2 efeB/phoH iron uptake transporter deferrochelatase/peroxidase subunit/phosphate starvation‑inducible protein PhoH
* * ÷ NZ_CP009273 1088084 1088154 71 3 [1] [1] 2 pgaA/dgcT poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA/GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1098794 1098816 23 2 [1] [1] 2 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1103751 1103770 20 2 [1] [1] 3 mdoC glucans biosynthesis protein MdoC
* * ÷ NZ_CP009273 1114180 1114211 32 3 [1] [0] 2 yceJ cytochrome b
* * ÷ NZ_CP009273 1122048 1122058 11 2 [1] [1] 2 yceH YceH family protein
* * ÷ NZ_CP009273 1148411 1148455 45 2 [1] [1] 2 fabF beta‑ketoacyl‑ACP synthase II
* * ÷ NZ_CP009273 1193234 1193267 34 2 [1] [0] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1193709 1193753 45 2 [1] [1] 2 BW25113_RS05920/lit hypothetical protein/cell death peptidase Lit
* * ÷ NZ_CP009273 1194086 1194138 53 2 [1] [1] 2 BW25113_RS05920/lit hypothetical protein/cell death peptidase Lit
* * ÷ NZ_CP009273 1207166 1207181 16 2 [0] [1] 2 iraM anti‑adapter protein IraM
* * ÷ NZ_CP009273 1207311 1207336 26 2 [0] [1] 2 iraM anti‑adapter protein IraM
* * ÷ NZ_CP009273 1207528 1207538 11 2 [0] [1] 2 iraM/BW25113_RS25985 anti‑adapter protein IraM/protein YmgK
* * ÷ NZ_CP009273 1211111 1211169 59 2 [0] [1] 2 bluF/ycgZ blue light‑responsive regulator BluF/regulatory protein YcgZ
* * ÷ NZ_CP009273 1215373 1215392 20 2 [1] [0] 2 BW25113_RS06070/BW25113_RS25990 hypothetical protein/autotransporter outer membrane beta‑barrel domain‑containing protein
* * ÷ NZ_CP009273 1218116 1218142 27 2 [1] [1] 2 ymgG glycine zipper domain‑containing protein
* * ÷ NZ_CP009273 1219737 1219823 87 2 [1] [1] 2 minE cell division topological specificity factor MinE
* * ÷ NZ_CP009273 1225839 1225872 34 2 [1] [1] 3 [hlyE] [hlyE]
* * ÷ NZ_CP009273 1233556 1233600 45 2 [1] [1] 2 dadA D‑amino acid dehydrogenase
* * ÷ NZ_CP009273 1238471 1238474 4 2 [1] [1] 2 ldcA muramoyltetrapeptide carboxypeptidase
* * ÷ NZ_CP009273 1249834 1249873 40 2 [0] [1] 2 ycgV autotransporter outer membrane beta‑barrel domain‑containing protein
* * ÷ NZ_CP009273 1276975 1277002 28 2 [1] [1] 2 narG nitrate reductase subunit alpha
* * ÷ NZ_CP009273 1279340 1279387 48 2 [1] [1] 2 narH nitrate reductase subunit beta
* * ÷ NZ_CP009273 1285651 1285669 19 2 [1] [0] 3 rssA/rssB patatin‑like phospholipase RssA/two‑component system response regulator RssB
* * ÷ NZ_CP009273 1295048 1295074 27 2 [1] [1] 2 BW25113_RS25865 hypothetical protein
* * ÷ NZ_CP009273 1301516 1301517 2 2 [0] [0] 2 cls cardiolipin synthase
* * ÷ NZ_CP009273 1305425 1305435 11 3 [1] [0] 2 tonB TonB system transport protein TonB
* * ÷ NZ_CP009273 1316357 1316390 34 3 [0] [1] 2 trpE anthranilate synthase component I
* * ÷ NZ_CP009273 1320250 1320260 11 3 [0] [0] 2 yciQ DUF2207 domain‑containing protein
* * ÷ NZ_CP009273 1323807 1323844 38 3 [1] [1] 3 sohB protease SohB
* * ÷ NZ_CP009273 1324141 1324160 20 2 [0] [1] 2 sohB protease SohB
* * ÷ NZ_CP009273 1327698 1327824 127 3 [1] [1] 3 topA type I DNA topoisomerase
* * ÷ NZ_CP009273 1333864 1334003 140 3 [1] [1] 2 pgpB phosphatidylglycerophosphatase B
* * ÷ NZ_CP009273 1337757 1337777 21 3 [0] [1] 2 osmB/yciT osmotically‑inducible lipoprotein OsmB/DNA‑binding transcriptional regulator YciT
* * ÷ NZ_CP009273 1345882 1345948 67 2 [1] [1] 2 ycjD DUF559 domain‑containing protein
* * ÷ NZ_CP009273 1384629 1384639 11 2 [1] [1] 2 mpaA murein tripeptide amidase MpaA
* * ÷ NZ_CP009273 1409373 1409398 26 3 [1] [1] 2 recE exodeoxyribonuclease VIII
* * ÷ NZ_CP009273 1418253 1418300 48 2 [0] [1] 2 trkG Trk system potassium transporter TrkG
* * ÷ NZ_CP009273 1524311 1524409 99 3 [1] [1] 2 [BW25113_RS26145] [BW25113_RS26145]
* * ÷ NZ_CP009273 1592421 1592424 4 2 [0] [0] 2 BW25113_RS07915/lsrK ECSE_1600 family autotransporter/autoinducer‑2 kinase
* * ÷ NZ_CP009273 1618836 1618909 74 3 [1] [0] 2 ydeI/ydeJ YdeI family stress tolerance OB fold protein/2‑oxo‑tetronate isomerase
* * ÷ NZ_CP009273 1619017 1619046 30 2 [1] [1] 2 [ydeJ] [ydeJ]
* * ÷ NZ_CP009273 1631300 1631314 15 2 [1] [1] 2 [ydfO] [ydfO]
* * ÷ NZ_CP009273 1663580 1663583 4 2 [1] [0] 3 ynfL LysR family transcriptional regulator
* * ÷ NZ_CP009273 1673740 1673761 22 3 [0] [1] 2 ydgH/ydgI DUF1471 family protein YdgH/amino acid permease
* * ÷ NZ_CP009273 1807508 1807561 54 2 [1] [1] 2 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1980151 1980204 54 2 [1] [1] 2 araF/ftnB arabinose ABC transporter substrate‑binding protein AraF/non‑heme ferritin‑like protein
* * ÷ NZ_CP009273 2185859 2185873 15 5 [1] [0] 2 yehD/yehE fimbrial protein/YehE family protein
* * ÷ NZ_CP009273 2222347 2222391 45 2 [0] [1] 2 mdtQ/yohP multidrug resistance outer membrane protein MdtQ/protein YohP
* * ÷ NZ_CP009273 2357865 2357915 51 2 [1] [1] 3 yfaZ/nudI YfaZ family protein/nucleoside triphosphatase NudI
* * ÷ NZ_CP009273 2368167 2368236 70 2 [1] [1] 3 menE o‑succinylbenzoate‑‑CoA ligase
* * ÷ NZ_CP009273 2462787 2462818 32 2 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2491883 2491914 32 2 [0] [1] 3 alaC/ypdA alanine transaminase/two‑component system sensor histidine kinase YpdA
* * ÷ NZ_CP009273 2563828 2563838 11 3 [0] [1] 3 eutE aldehyde dehydrogenase EutE
* * ÷ NZ_CP009273 2567308 2567323 16 3 [1] [0] 4 eutT ethanolamine utilization cob(I)yrinic acid a,c‑diamide adenosyltransferase EutT
* * ÷ NZ_CP009273 2897140 2897184 45 2 [1] [1] 2 ygcE/queE FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NZ_CP009273 2982220 2982230 11 3 [0] [1] 4 yqeI transcriptional regulator
* * ÷ NZ_CP009273 3183980 3183990 11 3 [1] [1] 2 [yqiH] [yqiH]
* * ÷ NZ_CP009273 3347815 3347820 6 2 [1] [0] 2 yhcC/gltB TIGR01212 family radical SAM protein/glutamate synthase large subunit
* * ÷ NZ_CP009273 3354473 3354483 11 4 [0] [1] 4 gltD/gltF glutamate synthase subunit GltD/DUF1120 domain‑containing protein
* * ÷ NZ_CP009273 3644567 3644570 4 2 [0] [0] 4 arsC/BW25113_RS18155 glutaredoxin‑dependent arsenate reductase/hypothetical protein
* * ÷ NZ_CP009273 3747848 3747864 17 2 [1] [1] 2 yiaW/BW25113_RS25895 DUF3302 domain‑containing protein/hypothetical protein
* * ÷ NZ_CP009273 3797716 3797726 11 3 [0] [1] 3 rfaS LPS core biosynthesis protein RfaS

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)42 (2.530) 23/166 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 = 12032619 (0.540)9 (0.670) 8/134 0.4 68.5% coding (305/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 = 1205058 1 (0.070)coding (57/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)8 (0.490) 5/164 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 = 19727510 (0.000)14 (0.840) 11/166 0.3 100% 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 4532499 =5 (0.300)8 (0.540) 6/148 0.7 60.5% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 6 (0.410)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
* ? NZ_CP009273 = 45325075 (0.300)5 (0.340) 5/148 0.8 48.9% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 6 (0.410)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA