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 226,010 (A)6→5 coding (357/804 nt) dkgB → 2,5‑didehydrogluconate reductase DkgB
RA 859,587 G→A A164T (GCA→ACA)  fsa → fructose‑6‑phosphate aldolase
RA 1,613,627 T→A V84E (GTG→GAG)  marR → multiple antibiotic resistance transcriptional regulator MarR
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,631,337 G→A W112* (TGG→TGA)  pitA → inorganic phosphate transporter PitA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 279632 279642 11 2 [0] [1] 2 yagF xylonate dehydratase YagF
* * ÷ NZ_CP009273 356938 357593 656 5 [0] [1] 5 lacA lacA
* * ÷ NZ_CP009273 428520 428524 5 2 [0] [0] 2 nrdR transcriptional regulator NrdR
* * ÷ NZ_CP009273 671830 672400 571 17 [1] [1] 2 [ybeQ]–[ybeR] [ybeQ],[ybeR]
* * ÷ NZ_CP009273 672479 672665 187 2 [1] [1] 2 ybeR DUF1266 domain‑containing protein
* * ÷ NZ_CP009273 672730 673950 1221 2 [1] [1] 3 [ybeR]–[djlB] [ybeR],[djlB]
* * ÷ NZ_CP009273 674003 675960 1958 3 [1] [1] 2 [djlB]–[djlC] [djlB],ybeT,ybeU,[djlC]
* * ÷ NZ_CP009273 676195 677181 987 2 [1] [0] 2 [djlC]–[hscC] [djlC],[hscC]
* * ÷ NZ_CP009273 677220 677697 478 2 [0] [1] 2 hscC molecular chaperone HscC
* * ÷ NZ_CP009273 677941 678154 214 2 [1] [0] 2 hscC molecular chaperone HscC
* * ÷ NZ_CP009273 678228 678587 360 3 [1] [0] 2 hscC molecular chaperone HscC
* * ÷ NZ_CP009273 678672 678863 192 2 [0] [1] 2 [hscC] [hscC]
* * ÷ NZ_CP009273 678917 679458 542 2 [1] [1] 2 [rihA] [rihA]
* * ÷ NZ_CP009273 679549 680150 602 2 [1] [1] 2 [rihA]–[gltL] [rihA],[gltL]
* * ÷ NZ_CP009273 680180 680573 394 2 [1] [1] 2 gltL glutamate/aspartate ABC transporter ATP‑binding protein GltL
* * ÷ NZ_CP009273 680658 680717 60 2 [1] [1] 2 [gltL]–[gltK] [gltL],[gltK]
* * ÷ NZ_CP009273 680867 680951 85 2 [1] [1] 2 gltK glutamate/aspartate ABC transporter permease GltK
* * ÷ NZ_CP009273 681042 681970 929 2 [1] [1] 2 [gltK]–[gltJ] [gltK],[gltJ]
* * ÷ NZ_CP009273 681997 682113 117 2 [1] [1] 2 gltJ glutamate/aspartate ABC transporter permease GltJ
* * ÷ NZ_CP009273 682156 682302 147 2 [1] [1] 2 [gltI] [gltI]
* * ÷ NZ_CP009273 682319 682442 124 2 [1] [1] 2 gltI glutamate/aspartate ABC transporter substrate‑binding protein GltI
* * ÷ NZ_CP009273 682513 682567 55 2 [1] [1] 2 gltI glutamate/aspartate ABC transporter substrate‑binding protein GltI
* * ÷ NZ_CP009273 682628 682737 110 2 [1] [0] 2 gltI glutamate/aspartate ABC transporter substrate‑binding protein GltI
* * ÷ NZ_CP009273 682794 682908 115 3 [1] [1] 2 gltI glutamate/aspartate ABC transporter substrate‑binding protein GltI
* * ÷ NZ_CP009273 682956 683196 241 2 [1] [0] 2 gltI glutamate/aspartate ABC transporter substrate‑binding protein GltI
* * ÷ NZ_CP009273 683270 683295 26 2 [0] [1] 2 gltI/BW25113_RS03405 glutamate/aspartate ABC transporter substrate‑binding protein GltI/IS5‑like element IS5 family transposase
* * ÷ NZ_CP009273 885996 886031 36 2 [1] [1] 2 grxA glutaredoxin 1
* * ÷ NZ_CP009273 950164 950235 72 3 [0] [1] 2 focA/ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 1094671 1094679 9 3 [1] [1] 2 ycdX zinc‑binding phosphatase
* * ÷ NZ_CP009273 1161484 1161501 18 4 [0] [0] 2 ycfP/ndh alpha/beta hydrolase YcfP/NADH‑quinone dehydrogenase
* * ÷ NZ_CP009273 1164370 1164434 65 2 [1] [1] 2 comR/bhsA TetR family copper‑responsive transcriptional repressor ComR/multiple stress resistance protein BhsA
* * ÷ NZ_CP009273 1172267 1172369 103 3 [1] [0] 2 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1207824 1207849 26 3 [0] [1] 3 BW25113_RS25985/BW25113_RS25535 protein YmgK/hypothetical protein
* * ÷ NZ_CP009273 1208480 1208488 9 2 [1] [0] 2 ycgX DUF1398 domain‑containing protein
* * ÷ NZ_CP009273 1212100 1212139 40 2 [1] [1] 2 ariR/BW25113_RS06060 biofilm/acid‑resistance regulator AriR/hypothetical protein
* * ÷ NZ_CP009273 1225963 1226003 41 2 [1] [1] 3 hlyE/umuD hemolysin HlyE/translesion error‑prone DNA polymerase V autoproteolytic subunit
* * ÷ NZ_CP009273 1354136 1354217 82 2 [1] [1] 3 puuA glutamate‑putrescine ligase
* * ÷ NZ_CP009273 1366047 1366072 26 4 [1] [1] 2 ycjM glucosylglycerate phosphorylase
* * ÷ NZ_CP009273 1372368 1372394 27 3 [0] [1] 2 ycjT kojibiose phosphorylase
* * ÷ NZ_CP009273 1387340 1387365 26 2 [0] [1] 2 pgrR/mppA DNA‑binding transcriptional regulator PgrR/murein tripeptide ABC transporter substrate‑binding protein MppA
* * ÷ NZ_CP009273 1424340 1424348 9 3 [0] [1] 2 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1424481 1424566 86 2 [1] [1] 2 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1424660 1424664 5 2 [0] [0] 8 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1485771 1485795 25 2 [0] [1] 3 cybB/BW25113_RS07445 cytochrome b561/periplasmic protein
* * ÷ NZ_CP009273 1524250 1524337 88 2 [0] [1] 3 BW25113_RS07645/BW25113_RS26145 RHS repeat protein/hypothetical protein
* * ÷ NZ_CP009273 1539038 1539038 1 2 [0] [0] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1540296 1540363 68 2 [0] [1] 3 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1578201 1578257 57 2 [1] [1] 2 [safA] [safA]
* * ÷ NZ_CP009273 1600749 1600766 18 2 [1] [1] 2 lsrF 3‑hydroxy‑5‑phosphonooxypentane‑2,4‑dione thiolase
* * ÷ NZ_CP009273 1610093 1610121 29 2 [1] [1] 2 yneK putative protein YneK
* * ÷ NZ_CP009273 1711237 1711270 34 2 [1] [1] 2 tyrS tyrosine‑‑tRNA ligase
* * ÷ NZ_CP009273 1728900 1728935 36 3 [1] [1] 2 mepH peptidoglycan DD‑endopeptidase MepH
* * ÷ NZ_CP009273 1749069 1749084 16 2 [1] [1] 2 ydhY/fumD ferredoxin‑like protein/fumarate hydratase FumD
* * ÷ NZ_CP009273 1780353 1780363 11 4 [0] [0] 2 ppsA phosphoenolpyruvate synthase
* * ÷ NZ_CP009273 1806963 1806972 10 2 [0] [1] 3 BW25113_RS09050 hypothetical protein
* * ÷ NZ_CP009273 1807065 1807087 23 3 [1] [1] 2 BW25113_RS09050 hypothetical protein
* * ÷ NZ_CP009273 1813710 1813712 3 2 [0] [1] 2 [chbA] [chbA]
* * ÷ NZ_CP009273 1952565 1952596 32 2 [1] [1] 2 torY/cutC NapC/NirT family cytochrome c/copper homeostasis protein CutC
* * ÷ NZ_CP009273 2009229 2009245 17 3 [1] [0] 3 fliG flagellar motor switch protein FliG
* * ÷ NZ_CP009273 2097486 2097576 91 2 [1] [0] 2 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2144553 2144613 61 2 [1] [1] 2 yegI/yegJ protein kinase YegI/DUF2314 domain‑containing protein
* * ÷ NZ_CP009273 2185859 2185916 58 3 [1] [1] 3 yehD/yehE fimbrial protein/YehE family protein
* * ÷ NZ_CP009273 2357896 2357934 39 3 [1] [1] 2 yfaZ/nudI YfaZ family protein/nucleoside triphosphatase NudI
* * ÷ NZ_CP009273 2463140 2463154 15 2 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2505238 2505259 22 2 [1] [1] 2 mntH Nramp family divalent metal transporter
* * ÷ NZ_CP009273 2753647 2753682 36 2 [1] [1] 2 yfjI YfjI family protein
* * ÷ NZ_CP009273 2768290 2768302 13 2 [1] [1] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2897061 2897114 54 3 [0] [1] 2 ygcE/queE FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
* * ÷ NZ_CP009273 2988546 2988576 31 2 [0] [1] 3 BW25113_RS14850/BW25113_RS26010 response regulator transcription factor/hypothetical protein
* * ÷ NZ_CP009273 3262540 3262575 36 2 [1] [1] 2 yhaC YhaC family protein
* * ÷ NZ_CP009273 3280460 3280470 11 2 [0] [0] 2 agaI/yraH galactosamine‑6‑phosphate isomerase/fimbrial protein
* * ÷ NZ_CP009273 3661067 3661076 10 2 [0] [1] 2 gadA/ccp glutamate decarboxylase/cytochrome c peroxidase
* * ÷ NZ_CP009273 3798120 3798169 50 2 [1] [1] 2 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 269666 =NA (NA)16 (0.870) 10/166 0.5 94.1% intergenic (+2/+146) ykfC/BW25113_RS01325 reverse transcriptase domain‑containing protein/IS5‑like element IS5 family transposase
?NZ_CP009273 = 671829 1 (0.050)coding (175/978 nt) ybeQ SEL1‑like repeat protein
* ? NZ_CP009273 360104 =NA (NA)18 (0.980) 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 = 1391494NA (NA)9 (0.490) 5/164 1.1 100% 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)21 (1.140) 18/166 0.1 100% 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 = 45325076 (0.330)6 (0.370) 5/148 1.0 47.3% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 8 (0.490)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA