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 50,102 A→C I94L (ATT→CTT)  folA → type 3 dihydrofolate reductase
RA 1,858,499 G→C W131C (TGG→TGC)  yeaD → D‑hexose‑6‑phosphate mutarotase
RA 2,236,491 A→C F214C (TTT→TGT)  folE ← GTP cyclohydrolase I FolE
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 4,171,725 G→C D185H (GAC→CAC)  rpoB → DNA‑directed RNA polymerase subunit beta

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 295437 295481 45 2 [1] [1] 2 paoC aldehyde oxidoreductase molybdenum‑binding subunit PaoC
* * ÷ NZ_CP009273 295808 295833 26 2 [1] [1] 4 paoC aldehyde oxidoreductase molybdenum‑binding subunit PaoC
* * ÷ NZ_CP009273 356969 357568 600 2 [1] [1] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 529782 529794 13 2 [1] [0] 2 gcl glyoxylate carboligase
* * ÷ NZ_CP009273 565412 565454 43 2 [1] [1] 2 ybcK recombinase family protein
* * ÷ NZ_CP009273 603129 603173 45 2 [1] [0] 2 ybdK/hokE YbdK family carboxylate‑amine ligase/type I toxin‑antitoxin system toxin HokE
* * ÷ NZ_CP009273 635842 635851 10 2 [1] [0] 3 ahpF alkyl hydroperoxide reductase subunit F
* * ÷ NZ_CP009273 647613 647630 18 2 [1] [1] 2 citC/dpiB [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
* * ÷ NZ_CP009273 745008 745018 11 2 [0] [1] 2 ybgP molecular chaperone
* * ÷ NZ_CP009273 772595 772653 59 2 [1] [1] 2 tolA cell envelope integrity protein TolA
* * ÷ NZ_CP009273 817795 817803 9 2 [1] [1] 3 ybhN YbhN family protein
* * ÷ NZ_CP009273 950063 950255 193 2 [0] [1] 3 focA/ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 982484 982510 27 2 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 982811 982923 113 3 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 1075169 1075184 16 2 [1] [0] 3 putP sodium/proline symporter PutP
* * ÷ NZ_CP009273 1133290 1133324 35 3 [1] [0] 2 flgJ flagellar assembly peptidoglycan hydrolase FlgJ
* * ÷ NZ_CP009273 1161415 1161534 120 4 [1] [1] 2 ycfP/ndh alpha/beta hydrolase YcfP/NADH‑quinone dehydrogenase
* * ÷ NZ_CP009273 1351091 1351149 59 2 [1] [1] 4 sapA peptide ABC transporter substrate‑binding protein SapA
* * ÷ NZ_CP009273 1459415 1459425 11 2 [0] [0] 2 [BW25113_RS25580] [BW25113_RS25580]
* * ÷ NZ_CP009273 1459506 1459573 68 2 [0] [1] 2 BW25113_RS25580/BW25113_RS07350 hypothetical protein/autotransporter domain‑containing protein
* * ÷ NZ_CP009273 1557757 1557767 11 5 [0] [1] 3 dosP oxygen‑sensing cyclic‑di‑GMP phosphodiesterase
* * ÷ NZ_CP009273 1566410 1566452 43 2 [1] [0] 2 gadB/pqqL glutamate decarboxylase/insulinase family protein
* * ÷ NZ_CP009273 1566507 1566598 92 2 [0] [1] 3 gadB/pqqL glutamate decarboxylase/insulinase family protein
* * ÷ NZ_CP009273 1568239 1568270 32 2 [1] [1] 2 pqqL insulinase family protein
* * ÷ NZ_CP009273 1635258 1635285 28 2 [1] [1] 7 ynfU/cspB putative zinc‑binding protein YnfU/cold shock‑like protein CspB
* * ÷ NZ_CP009273 1649299 1649325 27 2 [1] [1] 2 rspA starvation‑sensing protein RspA
* * ÷ NZ_CP009273 1687145 1687151 7 2 [0] [1] 2 [uidB] [uidB]
* * ÷ NZ_CP009273 1691720 1691833 114 2 [1] [1] 2 hdhA 7‑alpha‑hydroxysteroid dehydrogenase
* * ÷ NZ_CP009273 1728876 1728938 63 2 [1] [1] 2 mepH peptidoglycan DD‑endopeptidase MepH
* * ÷ NZ_CP009273 1760717 1760749 33 3 [1] [0] 2 ydiJ FAD‑binding and (Fe‑S)‑binding domain‑containing protein
* * ÷ NZ_CP009273 1775766 1775776 11 2 [0] [1] 3 ydiS FAD‑dependent oxidoreductase
* * ÷ NZ_CP009273 1786926 1786974 49 2 [1] [0] 3 nlpC NlpC/P60 family protein
* * ÷ NZ_CP009273 1792936 1792962 27 2 [1] [1] 3 pheS phenylalanine‑‑tRNA ligase subunit alpha
* * ÷ NZ_CP009273 1800550 1800564 15 2 [0] [1] 3 ydiY/pfkB YdiY family protein/6‑phosphofructokinase II
* * ÷ NZ_CP009273 1807508 1807567 60 2 [1] [1] 2 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1816007 1816007 1 3 [0] [0] 8 chbB/osmE PTS N,N'‑diacetylchitobiose transporter subunit IIB/osmotically‑inducible lipoprotein OsmE
* * ÷ NZ_CP009273 1841636 1841674 39 2 [1] [0] 3 selD selenide, water dikinase SelD
* * ÷ NZ_CP009273 1863381 1863396 16 3 [1] [1] 6 yeaH YeaH/YhbH family protein
* * ÷ NZ_CP009273 1864700 1864750 51 2 [1] [1] 2 cdgI GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1877259 1877280 22 2 [1] [1] 2 dmlA/yeaV multifunctional D‑malate/3‑isopropylmalate/tartarate dehydrogenase/BCCT family transporter YeaV
* * ÷ NZ_CP009273 1888048 1888129 82 2 [0] [1] 3 yoaB/yoaC RidA family protein/DUF1889 family protein
* * ÷ NZ_CP009273 1890525 1890573 49 3 [1] [1] 2 nudL CoA pyrophosphatase
* * ÷ NZ_CP009273 1899630 1899684 55 3 [1] [1] 2 yobD/mntP DUF986 family protein/manganese efflux pump MntP
* * ÷ NZ_CP009273 2027407 2027418 12 3 [1] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2096990 2097016 27 2 [1] [1] 2 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2181175 2181185 11 2 [1] [1] 2 yehA putative fimbrial‑like adhesin protein
* * ÷ NZ_CP009273 2185791 2185871 81 4 [1] [1] 2 yehD/yehE fimbrial protein/YehE family protein
* * ÷ NZ_CP009273 2222525 2222536 12 3 [1] [1] 2 yohP protein YohP
* * ÷ NZ_CP009273 2297175 2297195 21 2 [0] [0] 6 BW25113_RS25870 hypothetical protein
* * ÷ NZ_CP009273 2463636 2463769 134 2 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2505218 2505287 70 2 [0] [1] 2 mntH Nramp family divalent metal transporter
* * ÷ NZ_CP009273 2622963 2623027 65 2 [1] [0] 2 yfgG/yfgH YfgG family protein/glycine zipper 2TM domain‑containing protein
* * ÷ NZ_CP009273 2628285 2628308 24 2 [0] [1] 2 xseA exodeoxyribonuclease VII large subunit
* * ÷ NZ_CP009273 2646992 2647002 11 3 [1] [0] 2 sseA/timP 3‑mercaptopyruvate sulfurtransferase/small toxic inner membrane protein TimP
* * ÷ NZ_CP009273 2696906 2696941 36 2 [1] [1] 2 rnc ribonuclease III
* * ÷ NZ_CP009273 3261752 3261773 22 2 [1] [0] 2 [BW25113_RS16190] [BW25113_RS16190]
* * ÷ NZ_CP009273 3454158 3454168 11 2 [1] [0] 3 gspF type II secretion system inner membrane protein GspF
* * ÷ NZ_CP009273 3629063 3630136 1074 22 [0] [1] 2 [yhiM]–[yhiN] [yhiM],[yhiN]
* * ÷ NZ_CP009273 3630221 3638744 8524 2 [1] [0] 2 [yhiN]–prlC [yhiN],pitA,uspB,uspA,BW25113_RS26225,BW25113_RS26230,dtpB,rsmJ,prlC
* * ÷ NZ_CP009273 3638790 3640700 1911 2 [0] [1] 2 [rlmJ]–[gorA] [rlmJ],[gorA]
* * ÷ NZ_CP009273 3640791 3641332 542 2 [1] [1] 2 [gorA]–dinQ [gorA],dinQ
* * ÷ NZ_CP009273 3641371 3643999 2629 2 [1] [1] 2 arsR–[arsC] arsR,arsB,[arsC]
* * ÷ NZ_CP009273 3644053 3644831 779 2 [1] [0] 2 [BW25113_RS18155] [BW25113_RS18155]
* * ÷ NZ_CP009273 3644880 3646531–3645397 518–1652 2 [0] [1] 2 [BW25113_RS18155]–BW25113_RS18160 [BW25113_RS18155],BW25113_RS18160
* * ÷ NZ_CP009273 4466811 4466859 49 2 [1] [1] 2 BW25113_RS22080 hypothetical protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)19 (1.270) 15/168 0.1 59.4% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 13 (0.870)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 2282398 =NA (NA)21 (1.410) 13/168 0.2 100% pseudogene (3/2532 nt) yejO autotransporter YejO
?NZ_CP009273 = 3629062 0 (0.000)coding (862/1053 nt) yhiM DUF2776 domain‑containing protein
* ? NZ_CP009273 4532499 =0 (0.000)6 (0.450) 5/150 0.8 92.3% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 1 (0.080)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
* ? NZ_CP009273 = 45325070 (0.000)11 (0.830) 11/150 0.2 95.7% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 1 (0.080)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA