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 357570 590 3 [0] [1] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 380257 380274 18 3 [1] [1] 2 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 418957 418994 38 2 [1] [1] 2 malZ maltodextrin glucosidase
* * ÷ NZ_CP009273 428510 428585 76 2 [1] [1] 3 nrdR transcriptional regulator NrdR
* * ÷ NZ_CP009273 579510 579597 88 2 [1] [1] 2 appY DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 716391 716433 43 4 [0] [1] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 729528 729552 25 3 [1] [1] 2 BW25113_RS03630 hypothetical protein
* * ÷ NZ_CP009273 732255 732275 21 2 [1] [1] 3 ybfQ/BW25113_RS03650 ISAs1 family transposase/ISAs1 family transposase
* * ÷ NZ_CP009273 733473–733501 733512 12–40 2 [1] [1] 3 BW25113_RS03650/ybfD ISAs1 family transposase/ISAs1 family transposase
* * ÷ NZ_CP009273 806228 806235 8 2 [1] [1] 2 bioF 8‑amino‑7‑oxononanoate synthase
* * ÷ NZ_CP009273 845800 845831 32 3 [0] [1] 2 BW25113_RS25505 protein YliM
* * ÷ NZ_CP009273 886605 886615 11 3 [0] [1] 3 ybjC DUF1418 family protein
* * ÷ NZ_CP009273 902712 902722 11 2 [1] [1] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 993098 993137 40 3 [0] [0] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1136725 1136748 24 2 [0] [1] 2 rne ribonuclease E
* * ÷ NZ_CP009273 1158254 1158289 36 2 [1] [1] 3 lpoB penicillin‑binding protein activator LpoB
* * ÷ NZ_CP009273 1185151 1185166 16 3 [1] [1] 2 phoQ two‑component system sensor histidine kinase PhoQ
* * ÷ NZ_CP009273 1210243 1210281 39 2 [1] [1] 3 bluF blue light‑responsive regulator BluF
* * ÷ NZ_CP009273 1224991 1225003 13 2 [0] [1] 3 hlyE hemolysin HlyE
* * ÷ NZ_CP009273 1267321 1267349 29 2 [1] [1] 2 chaA/chaB sodium‑potassium/proton antiporter ChaA/putative cation transport regulator ChaB
* * ÷ NZ_CP009273 1281074 1281103 30 2 [1] [1] 2 narJ nitrate reductase molybdenum cofactor assembly chaperone
* * ÷ NZ_CP009273 1287895 1287907 13 2 [1] [0] 4 galU/hns UTP‑‑glucose‑1‑phosphate uridylyltransferase GalU/DNA‑binding transcriptional regulator H‑NS
* * ÷ NZ_CP009273 1320896 1320939 44 2 [1] [1] 2 [yciQ] [yciQ]
* * ÷ NZ_CP009273 1327981 1327990 10 3 [0] [1] 2 topA/cysB type I DNA topoisomerase/HTH‑type transcriptional regulator CysB
* * ÷ NZ_CP009273 1378896 1378921 26 2 [1] [1] 4 ycjX YcjX family protein
* * ÷ NZ_CP009273 1379086 1379122 37 2 [1] [1] 2 ycjX YcjX family protein
* * ÷ NZ_CP009273 1380929 1380980 52 3 [0] [1] 4 [tyrR] [tyrR]
* * ÷ NZ_CP009273 1424178 1424226 49 2 [1] [0] 2 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1424573 1424618 46 2 [1] [1] 2 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1441322 1441337 16 2 [0] [1] 2 feaR transcriptional regulator FeaR
* * ÷ NZ_CP009273 1446497 1446555 59 2 [1] [1] 2 paaZ phenylacetic acid degradation bifunctional protein PaaZ
* * ÷ NZ_CP009273 1494752 1494776 25 2 [1] [1] 2 ydcK/tehA YdcK family protein/dicarboxylate transporter/tellurite‑resistance protein TehA
* * ÷ NZ_CP009273 1499356 1499435 80 2 [1] [1] 2 ydcO BenE family transporter YdcO
* * ÷ NZ_CP009273 1524590 1524600 11 2 [1] [1] 3 BW25113_RS26145
BW25113_RS25600		 hypothetical protein
protein YncO
* * ÷ NZ_CP009273 1540174 1540217 44 2 [1] [0] 2 yddL porin
* * ÷ NZ_CP009273 1540271 1540468 198 2 [0] [1] 2 [yddL] [yddL]
* * ÷ NZ_CP009273 1580810 1580836 27 2 [1] [0] 2 ydeP/ydeQ acid resistance putative oxidoreductase YdeP/fimbrial protein
* * ÷ NZ_CP009273 1606397 1606402 6 2 [1] [1] 2 yneG DUF4186 domain‑containing protein
* * ÷ NZ_CP009273 1618892 1618930 39 2 [0] [1] 2 ydeI/ydeJ YdeI family stress tolerance OB fold protein/2‑oxo‑tetronate isomerase
* * ÷ NZ_CP009273 1631300 1631313 14 2 [0] [1] 2 [ydfO] [ydfO]
* * ÷ NZ_CP009273 1642474 1642474 1 4 [0] [0] 2 dicA DNA‑binding transcriptional dual regulator DicA
* * ÷ NZ_CP009273 1663646 1663740 95 3 [1] [1] 2 ynfL LysR family transcriptional regulator
* * ÷ NZ_CP009273 1680710 1680739 30 2 [1] [1] 3 fumC class II fumarate hydratase
* * ÷ NZ_CP009273 1691816 1691816 1 2 [0] [0] 2 hdhA 7‑alpha‑hydroxysteroid dehydrogenase
* * ÷ NZ_CP009273 1749652 1749668 17 2 [1] [1] 2 fumD/BW25113_RS26160 fumarate hydratase FumD/protein YnhH
* * ÷ NZ_CP009273 1807091 1807208 118 3 [1] [1] 2 BW25113_RS09050 hypothetical protein
* * ÷ NZ_CP009273 1820594 1820604 11 3 [1] [0] 2 astE succinylglutamate desuccinylase
* * ÷ NZ_CP009273 1864541 1864569 29 2 [0] [1] 2 yeaH/cdgI YeaH/YhbH family protein/GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1887688 1887696 9 3 [1] [1] 4 yoaB RidA family protein
* * ÷ NZ_CP009273 2052505 2052531 27 2 [1] [1] 2 yeeO toxic metabolite efflux MATE transporter YeeO
* * ÷ NZ_CP009273 2100474 2100505 32 3 [1] [1] 2 wzy O16 family O‑antigen polymerase
* * ÷ NZ_CP009273 2100676 2100714 39 3 [1] [1] 2 [wzy]–[glf] [wzy],[glf]
* * ÷ NZ_CP009273 2146645 2146653 9 2 [1] [0] 5 yegL/ibsA VWA domain‑containing protein/type I toxin‑antitoxin system toxin IbsA
* * ÷ NZ_CP009273 2149084 2149108 25 2 [1] [1] 2 mdtB multidrug efflux RND transporter permease subunit MdtB
* * ÷ NZ_CP009273 2185861 2185918 58 2 [1] [1] 2 yehD/yehE fimbrial protein/YehE family protein
* * ÷ NZ_CP009273 2249254 2249272 19 2 [1] [1] 5 yeiL transcriptional regulator YeiL
* * ÷ NZ_CP009273 2345589 2345599 11 2 [0] [1] 7 glpT glycerol‑3‑phosphate transporter
* * ÷ NZ_CP009273 2348065 2348087 23 2 [1] [0] 2 glpB glycerol‑3‑phosphate dehydrogenase subunit GlpB
* * ÷ NZ_CP009273 2505253 2505277 25 2 [1] [1] 2 mntH Nramp family divalent metal transporter
* * ÷ NZ_CP009273 2622990 2623002 13 2 [1] [1] 2 yfgG/yfgH YfgG family protein/glycine zipper 2TM domain‑containing protein
* * ÷ NZ_CP009273 2672212 2672216 5 2 [0] [0] 2 yphF substrate‑binding domain‑containing protein
* * ÷ NZ_CP009273 2696850 2696866 17 2 [1] [0] 2 rnc ribonuclease III
* * ÷ NZ_CP009273 2779384 2779398 15 3 [0] [1] 3 BW25113_RS13825/BW25113_RS26005 tRNA‑Ile/alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 2779845 2779881 37 2 [1] [1] 2 BW25113_RS26005 alpha‑amylase family glycosyl hydrolase
* * ÷ NZ_CP009273 3576442 3576452 11 4 [0] [1] 2 BW25113_RS17825 YrhA family protein
* * ÷ NZ_CP009273 4226572 4226594 23 3 [1] [1] 2 yjbF YjbF family lipoprotein
* * ÷ NZ_CP009273 4344748 4344754 7 2 [0] [1] 2 lysS/dtpC lysine‑‑tRNA ligase/dipeptide/tripeptide permease DtpC

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)60 (3.520) 27/168 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 1203246 =11 (0.650)9 (0.650) 9/136 0.3 51.6% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 8 (0.580)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)3 (0.180) 3/166 1.4 37.8% intergenic (+145/‑128) BW25113_RS06980/ynaJ IS5‑like element IS5 family transposase/DUF2534 family protein
?NZ_CP009273 1972747 = 5 (0.290)intergenic (‑293/‑487) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC