breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutation
evidence position mutation annotation gene description
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 356981 357569 589 3 [0] [1] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 380448 380507 60 2 [1] [1] 3 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 428524 428563 40 2 [0] [1] 3 nrdR transcriptional regulator NrdR
* * ÷ NZ_CP009273 497554 497603 50 3 [1] [1] 2 ybaL Kef family K(+) transporter
* * ÷ NZ_CP009273 508105 508140 36 2 [0] [1] 4 ybaT APC family permease
* * ÷ NZ_CP009273 508469 508504 36 2 [1] [1] 3 ybaT APC family permease
* * ÷ NZ_CP009273 510138 510182 45 2 [1] [1] 5 ybbJ NfeD family protein
* * ÷ NZ_CP009273 518463 518511 49 2 [1] [1] 3 ybbP/rhsD ABC transporter permease/rhs element protein RhsD
* * ÷ NZ_CP009273 524308 524368 61 3 [1] [1] 2 [BW25113_RS24960] [BW25113_RS24960]
* * ÷ NZ_CP009273 526014 526036 23 2 [1] [1] 2 mnmH tRNA 2‑selenouridine(34) synthase MnmH
* * ÷ NZ_CP009273 547805 547850 46 3 [1] [1] 2 purK 5‑(carboxyamino)imidazole ribonucleotide synthase
* * ÷ NZ_CP009273 553607 553612 6 2 [0] [1] 2 folD/fimA bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD/type 1 fimbrial major subunit FimA
* * ÷ NZ_CP009273 564325 564334 10 2 [0] [1] 4 BW25113_RS25485/ybcK hypothetical protein/recombinase family protein
* * ÷ NZ_CP009273 572470 572527 58 2 [1] [1] 2 BW25113_RS02855/essD porin/phage lysis protein EssD
* * ÷ NZ_CP009273 578807 578823 17 2 [1] [1] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 579009 579073 65 2 [1] [1] 4 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 579508 579582 75 2 [1] [1] 2 appY DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 618051 618061 11 3 [0] [0] 2 entS enterobactin transporter EntS
* * ÷ NZ_CP009273 651730 651798 69 2 [1] [1] 2 dcuC/pagP anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP
* * ÷ NZ_CP009273 652157 652166 10 2 [1] [0] 2 pagP lipid IV(A) palmitoyltransferase PagP
* * ÷ NZ_CP009273 656818 656897 80 4 [0] [1] 3 [ybeF] [ybeF]
* * ÷ NZ_CP009273 669223 669244 22 2 [0] [1] 2 leuS leucine‑‑tRNA ligase
* * ÷ NZ_CP009273 729141 729237 97 2 [0] [1] 2 [rhsC]–[BW25113_RS03630] [rhsC],[BW25113_RS03630]
* * ÷ NZ_CP009273 729533 729573 41 2 [0] [1] 2 [BW25113_RS03630] [BW25113_RS03630]
* * ÷ NZ_CP009273 733522 733540 19 2 [1] [0] 3 BW25113_RS03650/ybfD ISAs1 family transposase/ISAs1 family transposase
* * ÷ NZ_CP009273 748273 748304 32 4 [1] [1] 2 ybgD/gltA fimbrial protein/citrate synthase
* * ÷ NZ_CP009273 748374 748468 95 2 [1] [1] 3 ybgD/gltA fimbrial protein/citrate synthase
* * ÷ NZ_CP009273 753540 753558 19 2 [1] [1] 3 sdhB succinate dehydrogenase iron‑sulfur subunit SdhB
* * ÷ NZ_CP009273 766493 766590 98 2 [1] [0] 4 mngB/cydA mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I
* * ÷ NZ_CP009273 805777 805858 82 2 [1] [1] 3 [bioB]–[bioF] [bioB],[bioF]
* * ÷ NZ_CP009273 816193 816262 70 2 [1] [1] 2 [ybhM] [ybhM]
* * ÷ NZ_CP009273 850343 850346 4 2 [1] [1] 2 ldtB L,D‑transpeptidase
* * ÷ NZ_CP009273 856428 856442 15 2 [1] [1] 3 ybiW glycyl radical protein
* * ÷ NZ_CP009273 911677 911685 9 2 [0] [1] 2 aqpZ/ybjD aquaporin Z/ATP‑dependent endonuclease
* * ÷ NZ_CP009273 925694 925706 13 2 [0] [1] 2 cydD cysteine/glutathione ABC transporter permease/ATP‑binding protein CydD
* * ÷ NZ_CP009273 954500 954525 26 3 [1] [1] 2 aroA 3‑phosphoshikimate 1‑carboxyvinyltransferase
* * ÷ NZ_CP009273 954797 954804 8 2 [1] [1] 8 aroA 3‑phosphoshikimate 1‑carboxyvinyltransferase
* * ÷ NZ_CP009273 960378 960391 14 2 [1] [1] 2 ycaI ComEC family protein
* * ÷ NZ_CP009273 993098 993113 16 2 [1] [0] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 993857 993874 18 2 [1] [1] 2 [elfA] [elfA]
* * ÷ NZ_CP009273 1012388 1012450 63 3 [1] [1] 3 ycbZ Lon protease family protein
* * ÷ NZ_CP009273 1016537 1016565 29 2 [1] [0] 2 sulA/sxy cell division inhibitor SulA/CRP‑S regulon transcriptional coactivator Sxy
* * ÷ NZ_CP009273 1081847 1081869 23 2 [1] [1] 3 pgaD poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine biosynthesis protein PgaD
* * ÷ NZ_CP009273 1098844 1099010 167 2 [1] [1] 2 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1103653 1103677 25 2 [0] [1] 2 mdoC glucans biosynthesis protein MdoC
* * ÷ NZ_CP009273 1112588 1112623 36 3 [1] [1] 3 trhO rhodanese‑related sulfurtransferase
* * ÷ NZ_CP009273 1122215 1122280 66 2 [0] [1] 2 [yceH]–[yceM] [yceH],[yceM]
* * ÷ NZ_CP009273 1124093 1124233 141 3 [1] [1] 2 murJ murein biosynthesis integral membrane protein MurJ
* * ÷ NZ_CP009273 1128366 1128420 55 3 [1] [1] 3 flgE flagellar hook protein FlgE
* * ÷ NZ_CP009273 1146640 1146650 11 3 [1] [1] 2 fabG 3‑oxoacyl‑ACP reductase FabG
* * ÷ NZ_CP009273 1163689 1163712 24 3 [1] [1] 2 comR TetR family copper‑responsive transcriptional repressor ComR
* * ÷ NZ_CP009273 1165836 1165869 34 2 [1] [1] 2 ldtC/mfd L,D‑transpeptidase LdtC/transcription‑repair coupling factor
* * ÷ NZ_CP009273 1172277 1172350 74 2 [1] [0] 2 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1193189 1193218 30 2 [1] [1] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1208136 1208191 56 2 [1] [1] 2 [ycgX] [ycgX]
* * ÷ NZ_CP009273 1211502 1211559 58 2 [1] [1] 3 [ymgA] [ymgA]
* * ÷ NZ_CP009273 1211750 1211828 79 2 [1] [1] 2 [ymgA]–[ariR] [ymgA],[ariR]
* * ÷ NZ_CP009273 1212083 1212109 27 2 [0] [0] 2 [ariR] [ariR]
* * ÷ NZ_CP009273 1214440 1214483 44 2 [1] [1] 2 BW25113_RS06070 hypothetical protein
* * ÷ NZ_CP009273 1229330 1229347 18 3 [1] [1] 2 nhaB Na(+)/H(+) antiporter NhaB
* * ÷ NZ_CP009273 1235290 1235301 12 3 [1] [1] 3 dadX catabolic alanine racemase DadX
* * ÷ NZ_CP009273 1250314 1250425 112 2 [1] [1] 2 ycgV autotransporter outer membrane beta‑barrel domain‑containing protein
* * ÷ NZ_CP009273 1251513 1251515 3 3 [0] [0] 2 ycgV/ychF autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF
* * ÷ NZ_CP009273 1251669 1251767 99 2 [1] [0] 2 ycgV/ychF autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF
* * ÷ NZ_CP009273 1281389 1281400 12 2 [0] [1] 2 narI respiratory nitrate reductase subunit gamma
* * ÷ NZ_CP009273 1292607 1292650 44 2 [1] [1] 3 adhE bifunctional acetaldehyde‑CoA/alcohol dehydrogenase
* * ÷ NZ_CP009273 1303215 1303222 8 2 [0] [0] 3 [yciY] [yciY]
* * ÷ NZ_CP009273 1313651 1313678 28 2 [1] [1] 2 trpCF bifunctional indole‑3‑glycerol‑phosphate synthase TrpC/phosphoribosylanthranilate isomerase TrpF
* * ÷ NZ_CP009273 1327837 1327896 60 2 [1] [0] 2 topA type I DNA topoisomerase
* * ÷ NZ_CP009273 1334222 1334278 57 2 [1] [1] 2 pgpB phosphatidylglycerophosphatase B
* * ÷ NZ_CP009273 1355830 1355865 36 2 [0] [0] 2 puuD gamma‑glutamyl‑gamma‑aminobutyrate hydrolase
* * ÷ NZ_CP009273 1363734 1363748 15 2 [1] [0] 2 pspD phage shock protein PspD
* * ÷ NZ_CP009273 1370311 1370317 7 3 [0] [0] 2 ycjR sugar phosphate isomerase/epimerase
* * ÷ NZ_CP009273 1400096 1400119 24 2 [1] [0] 3 abgR/smrA LysR family transcriptional regulator/DNA endonuclease SmrA
* * ÷ NZ_CP009273 1410792 1410802 11 2 [1] [1] 3 recE exodeoxyribonuclease VIII
* * ÷ NZ_CP009273 1432362 1432365 4 3 [0] [0] 3 nifJ pyruvate:ferredoxin (flavodoxin) oxidoreductase
* * ÷ NZ_CP009273 1458454 1458489 36 2 [1] [1] 2 paaX phenylacetic acid degradation operon negative regulatory protein PaaX
* * ÷ NZ_CP009273 1459394 1459480 87 2 [0] [1] 2 [BW25113_RS25580] [BW25113_RS25580]
* * ÷ NZ_CP009273 1505658 1505669 12 3 [1] [1] 2 [ydcR] [ydcR]
* * ÷ NZ_CP009273 1524227 1524472 246 2 [1] [0] 2 [BW25113_RS26145] [BW25113_RS26145]
* * ÷ NZ_CP009273 1524609 1524618 10 2 [0] [0] 2 BW25113_RS26145
BW25113_RS25600
hypothetical protein
protein YncO
* * ÷ NZ_CP009273 1539063 1539252 190 2 [0] [1] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1539493 1539590 98 2 [1] [1] 2 BW25113_RS07710 leucine‑rich repeat domain‑containing protein
* * ÷ NZ_CP009273 1555013 1555128 116 2 [1] [1] 3 ddpB ABC transporter permease
* * ÷ NZ_CP009273 1625198 1625239 42 4 [0] [0] 2 ydfI/ydfJ mannitol dehydrogenase family protein/MHS family MFS transporter
* * ÷ NZ_CP009273 1631794 1631884 91 2 [1] [1] 2 [gnsB] [gnsB]
* * ÷ NZ_CP009273 1633083 1633148 66 2 [1] [0] 2 cspI/rzpQ cold shock protein CspI/DUF2514 domain‑containing protein
* * ÷ NZ_CP009273 1633376 1633453 78 2 [1] [1] 2 rzpQ DUF2514 domain‑containing protein
* * ÷ NZ_CP009273 1730077 1730107 31 2 [1] [0] 2 sodB superoxide dismutase [Fe]
* * ÷ NZ_CP009273 1751490 1751521 32 2 [0] [1] 2 pykF/lpp pyruvate kinase PykF/murein lipoprotein Lpp
* * ÷ NZ_CP009273 1754183 1754219 37 3 [1] [1] 3 sufS cysteine desulfurase SufS
* * ÷ NZ_CP009273 1765682 1765716 35 2 [1] [1] 3 ydiM MFS transporter
* * ÷ NZ_CP009273 1772538 1772558 21 2 [0] [0] 3 ydiO acyl‑CoA dehydrogenase
* * ÷ NZ_CP009273 1773007 1773100 94 2 [1] [1] 2 ydiP AraC family transcriptional regulator
* * ÷ NZ_CP009273 1807414 1807454 41 2 [0] [0] 2 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1815997 1816000 4 3 [0] [1] 3 chbB/osmE PTS N,N'‑diacetylchitobiose transporter subunit IIB/osmotically‑inducible lipoprotein OsmE
* * ÷ NZ_CP009273 1826266 1826307 42 2 [1] [0] 2 astC/xthA succinylornithine/acetylornithine transaminase/exodeoxyribonuclease III
* * ÷ NZ_CP009273 1833987 1834021 35 2 [1] [1] 2 ynjE thiosulfate sulfurtransferase YnjE
* * ÷ NZ_CP009273 1864825 1864870 46 2 [1] [0] 2 cdgI GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1881637 1881641 5 3 [0] [0] 2 rnd ribonuclease D
* * ÷ NZ_CP009273 1886542 1886559 18 2 [1] [1] 2 yoaA ATP‑dependent DNA helicase
* * ÷ NZ_CP009273 1899614 1899683 70 3 [1] [1] 2 yobD/mntP DUF986 family protein/manganese efflux pump MntP
* * ÷ NZ_CP009273 1919215 1919260 46 2 [1] [0] 2 [yobA] [yobA]
* * ÷ NZ_CP009273 1952479 1952556 78 2 [0] [1] 2 torY/cutC NapC/NirT family cytochrome c/copper homeostasis protein CutC
* * ÷ NZ_CP009273 1973014 1973024 11 2 [0] [1] 2 flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* * ÷ NZ_CP009273 1989097 1989193 97 3 [1] [0] 2 [BW25113_RS25650] [BW25113_RS25650]
* * ÷ NZ_CP009273 2092616 2092692 77 2 [1] [1] 3 ugd UDP‑glucose 6‑dehydrogenase
* * ÷ NZ_CP009273 2093220 2093276 57 2 [1] [1] 2 ugd/gndA UDP‑glucose 6‑dehydrogenase/NADP‑dependent phosphogluconate dehydrogenase
* * ÷ NZ_CP009273 2099581 2099605 25 3 [1] [0] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2100051 2100185 135 3 [1] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2101996 2102056 61 2 [1] [1] 2 wzx O16 family O‑antigen flippase
* * ÷ NZ_CP009273 2203952 2203966 15 2 [1] [0] 2 yehQ C69 family dipeptidase
* * ÷ NZ_CP009273 2462684 2462699 16 2 [0] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463243 2463261 19 3 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463719 2463768 50 3 [1] [1] 3 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2505277 2505277 1 2 [0] [0] 3 mntH Nramp family divalent metal transporter
* * ÷ NZ_CP009273 2622450 2622545 96 2 [1] [1] 3 [BW25113_RS25940] [BW25113_RS25940]
* * ÷ NZ_CP009273 2666830 2666840 11 7 [0] [1] 5 yphA DoxX family protein
* * ÷ NZ_CP009273 2767001 2767008 8 3 [1] [0] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2779798 2779816 19 2 [0] [0] 2 BW25113_RS26005 alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 2779863 2779902 40 2 [0] [1] 2 BW25113_RS26005 alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 2792343 2792355 13 2 [0] [0] 2 stpA/alaE DNA‑binding protein StpA/L‑alanine exporter AlaE
* * ÷ NZ_CP009273 2891092 2891109 18 2 [1] [1] 6 ygcS MFS transporter
* * ÷ NZ_CP009273 2983531 2983559 29 3 [1] [1] 3 BW25113_RS14820 hypothetical protein
* * ÷ NZ_CP009273 3751277 3751304 28 2 [1] [1] 3 yiaY/selB L‑threonine dehydrogenase/selenocysteine‑specific translation elongation factor
* * ÷ NZ_CP009273 4241606 4241636 31 3 [1] [1] 3 BW25113_RS20970 SopA family protein
* * ÷ NZ_CP009273 4241741 4241761 21 2 [1] [0] 2 BW25113_RS20970 SopA family protein
* * ÷ NZ_CP009273 4466822 4466853 32 2 [1] [0] 2 BW25113_RS22080 hypothetical protein
* * ÷ NZ_CP009273 4496361 4496371 11 5 [0] [1] 4 BW25113_RS25360 hypothetical protein
* * ÷ NZ_CP009273 4531648 4531714 67 3 [1] [1] 2 fimB/fimE type 1 fimbria switch DNA invertase FimB/type 1 fimbria switch DNA invertase FimE
* * ÷ NZ_CP009273 4532465 4532498 34 2 [1] [0] 9 fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)79 (4.810) 37/164 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 4532499 =0 (0.000)4 (0.270) 3/146 1.2 61.5% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 5 (0.340)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA