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 49,905 T→G L28R (CTC→CGC)  folA → type 3 dihydrofolate reductase
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 3,754,231 G→T R127S (CGC→AGC)  selA ← L‑seryl‑tRNA(Sec) selenium transferase
RA 3,776,510 A→G L171P (CTG→CCG)  gpsA ← NAD(P)H‑dependent glycerol‑3‑phosphate dehydrogenase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 234705 234762 58 2 [1] [1] 2 [BW25113_RS01095] [BW25113_RS01095]
* * ÷ NZ_CP009273 356981 357569 589 2 [0] [0] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 422676 422701 26 4 [1] [1] 2 tgt tRNA guanosine(34) transglycosylase Tgt
* * ÷ NZ_CP009273 508142 508150 9 2 [0] [1] 2 ybaT APC family permease
* * ÷ NZ_CP009273 716393 716452 60 2 [1] [1] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 764461 764507 47 2 [1] [1] 2 mngB mannosylglycerate hydrolase
* * ÷ NZ_CP009273 804337 804346 10 2 [1] [1] 2 bioA adenosylmethionine‑‑8‑amino‑7‑oxononanoate transaminase
* * ÷ NZ_CP009273 828697 828742 46 2 [1] [1] 2 dinG ATP‑dependent DNA helicase DinG
* * ÷ NZ_CP009273 835559 835569 11 3 [0] [1] 9 fiu catecholate siderophore receptor Fiu
* * ÷ NZ_CP009273 865331 865338 8 2 [0] [1] 3 gsiB glutathione ABC transporter substrate‑binding protein GsiB
* * ÷ NZ_CP009273 868426 868438 13 2 [0] [0] 2 [pdeI] [pdeI]
* * ÷ NZ_CP009273 871190 871209 20 2 [1] [1] 2 dgcI GGDEF domain‑containing protein
* * ÷ NZ_CP009273 877732 877774 43 2 [1] [1] 2 deoR DNA‑binding transcriptional repressor DeoR
* * ÷ NZ_CP009273 913643 913653 11 2 [0] [0] 2 ybjX VirK/YbjX family protein
* * ÷ NZ_CP009273 931355 931373 19 2 [1] [1] 3 ftsK DNA translocase FtsK
* * ÷ NZ_CP009273 950107 950176 70 2 [1] [0] 2 focA/ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 950509 950545 37 2 [1] [1] 2 ycaO 30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
* * ÷ NZ_CP009273 1021685 1021705 21 2 [1] [0] 2 helD DNA helicase IV
* * ÷ NZ_CP009273 1086256 1086312 57 2 [1] [0] 2 pgaA poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA
* * ÷ NZ_CP009273 1099567 1099580 14 2 [1] [1] 2 csgB curli minor subunit CsgB
* * ÷ NZ_CP009273 1099668 1099675 8 2 [1] [1] 3 csgB curli minor subunit CsgB
* * ÷ NZ_CP009273 1101646 1101649 4 4 [0] [0] 2 ymdB O‑acetyl‑ADP‑ribose deacetylase
* * ÷ NZ_CP009273 1116811 1116895 85 2 [1] [1] 2 dinI DNA damage‑inducible protein I
* * ÷ NZ_CP009273 1150097 1150105 9 2 [0] [1] 2 yceG cell division protein YceG
* * ÷ NZ_CP009273 1165747 1165754 8 2 [0] [0] 2 ldtC L,D‑transpeptidase LdtC
* * ÷ NZ_CP009273 1172096 1172136 41 2 [0] [1] 3 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1175219 1175235 17 2 [0] [0] 3 cobB NAD‑dependent protein deacylase
* * ÷ NZ_CP009273 1243250 1243257 8 2 [1] [1] 2 dhaM dihydroxyacetone kinase phosphoryl donor subunit DhaM
* * ÷ NZ_CP009273 1251756 1251778 23 2 [1] [1] 2 ycgV/ychF autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF
* * ÷ NZ_CP009273 1253600 1253604 5 2 [1] [0] 2 pth aminoacyl‑tRNA hydrolase
* * ÷ NZ_CP009273 1276782 1276815 34 2 [1] [1] 3 narG nitrate reductase subunit alpha
* * ÷ NZ_CP009273 1309867 1309922 56 2 [1] [1] 2 yciF ferritin‑like domain‑containing protein
* * ÷ NZ_CP009273 1348038 1348058 21 2 [1] [1] 2 sapC peptide ABC transporter permease SapC
* * ÷ NZ_CP009273 1375489 1375516 28 2 [1] [1] 3 BW25113_RS06905 ABC transporter ATP‑binding protein
* * ÷ NZ_CP009273 1384267 1384296 30 2 [1] [1] 3 mpaA murein tripeptide amidase MpaA
* * ÷ NZ_CP009273 1435318 1435340 23 2 [1] [1] 4 ydbJ DUF333 domain‑containing protein
* * ÷ NZ_CP009273 1757736 1757738 3 3 [0] [1] 2 sufB Fe‑S cluster assembly protein SufB
* * ÷ NZ_CP009273 1764424 1764456 33 2 [1] [1] 3 [ydiK] [ydiK]
* * ÷ NZ_CP009273 1881165 1881188 24 2 [1] [1] 2 rnd ribonuclease D
* * ÷ NZ_CP009273 1945241 1945251 11 2 [0] [1] 2 yecD hydrolase
* * ÷ NZ_CP009273 2001035 2001109 75 3 [1] [1] 2 amyA alpha‑amylase
* * ÷ NZ_CP009273 2149175 2149195 21 2 [0] [1] 2 mdtB multidrug efflux RND transporter permease subunit MdtB
* * ÷ NZ_CP009273 2178140 2178196 57 3 [1] [1] 2 thiM hydroxyethylthiazole kinase
* * ÷ NZ_CP009273 2212056 2212104 49 2 [1] [1] 2 osmF glycine betaine ABC transporter substrate‑binding protein OsmF
* * ÷ NZ_CP009273 2462999 2463050 52 3 [1] [1] 3 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 3628487 3646519–3645399 16913–18033 16 [0] [1] 3 [yhiM]–[BW25113_RS18160] [yhiM],yhiN,pitA,uspB,uspA,BW25113_RS26225,BW25113_RS26230,dtpB,rsmJ,prlC,rlmJ,gorA,dinQ,arsR,arsB,arsC,BW25113_RS18155,[BW25113_RS18160]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)27 (1.550) 18/168 0.1 37.5% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 45 (2.590)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 1203246 =11 (0.630)3 (0.210) 3/136 1.2 31.7% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 4 (0.280)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)11 (0.640) 5/166 1.0 100% 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 = 19727512 (0.120)23 (1.320) 13/168 0.2 92.0% 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 2282398 =NA (NA)16 (0.920) 13/168 0.2 100% pseudogene (3/2532 nt) yejO autotransporter YejO
?NZ_CP009273 = 3628486 0 (0.000)coding (286/1053 nt) yhiM DUF2776 domain‑containing protein
* ? NZ_CP009273 = 453250711 (0.630)5 (0.320) 5/150 0.9 27.9% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 16 (1.030)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA