mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 10,865 | A→C | G164G (GGT→GGG) | msyB ← | acidic protein MsyB |
| RA | 37,396 | T→C | A143A (GCA→GCG) | caiC ← | crotonobetaine/carnitine‑CoA ligase |
| RA | 37,524 | T→G | S101R (AGC→CGC) | caiC ← | crotonobetaine/carnitine‑CoA ligase |
| RA | 49,765 | C→T | intergenic (+134/‑58) | kefC → / → folA | glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase |
| RA | 49,910 | T→G | W30G (TGG→GGG) | folA → | type 3 dihydrofolate reductase |
| RA | 59,627 | C→A | intergenic (‑153/+60) | BW25113_RS25400 ← / ← rluA | transposase/bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA |
| RA | 75,122 | G→A | A339T (GCA→ACA) | setA → | sugar efflux transporter SetA |
| RA | 97,990 | A→C | T247P (ACC→CCC) | murC → | UDP‑N‑acetylmuramate‑‑L‑alanine ligase |
| RA | 115,634 | Δ1 bp | coding (415/552 nt) | ampD → | 1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase AmpD |
| RA | 232,843 | T→C | I97T (ATC→ACC) | dnaQ → | DNA polymerase III subunit epsilon |
| RA | 297,613 | (C)5→6 | coding (672/690 nt) | paoA ← | aldehyde dehydrogenase iron‑sulfur subunit |
| RA | 303,602 | T→G | N481T (AAC→ACC) | ecpC ← | fimbrial usher EcpC |
| RA | 338,646 | A→T | M18L (ATG→TTG) | yahK → | NADPH‑dependent aldehyde reductase YahK |
| RA | 351,491 | T→G | S287A (TCG→GCG) | codB → | cytosine permease |
| RA | 384,326 | A→C | G286G (GGT→GGG) | hemB ← | porphobilinogen synthase |
| RA | 393,907 | A→G | K194E (AAA→GAA) | yaiW → | surface‑exposed outer membrane lipoprotein YaiW |
| RA | 415,362 | T→C | S106P (TCC→CCC) | brnQ → | branched‑chain amino acid transporter carrier protein BrnQ |
| RA | 438,112 | A→G | S370G (AGC→GGC) | thiI → | tRNA 4‑thiouridine(8) synthase ThiI |
| RA | 441,095 | T→C | Y343C (TAC→TGC) | yajR ← | MFS transporter |
| RA | 446,387 | T→C | D227G (GAT→GGT) | cyoA ← | cytochrome o ubiquinol oxidase subunit II |
| RA | 467,406 | Δ1 bp | coding (1315/1782 nt) | mdlB → | SmdB family multidrug efflux ABC transporter permease/ATP‑binding protein |
| RA | 478,146 | A→C | F572V (TTT→GTT) | acrB ← | efflux RND transporter permease AcrB |
| RA | 525,225 | A→G | pseudogene (248/366 nt) | ylbG ← | helix‑turn‑helix domain‑containing protein |
| RA | 557,194 | A→G | Q681R (CAG→CGG) | sfmD → | fimbrial biogenesis usher protein |
| RA | 609,496 | A→C | L33F (TTA→TTC) | ybdZ → | enterobactin biosynthesis protein YbdZ |
| RA | 625,777 | A→G | D143G (GAC→GGC) | cstA → | pyruvate/proton symporter CstA |
| RA | 634,370 | A→C | intergenic (‑341/‑31) | dsbG ← / → ahpC | thiol:disulfide interchange protein DsbG/alkyl hydroperoxide reductase subunit C |
| RA | 659,797 | A→C | S284A (TCG→GCG) | rlpA ← | endolytic peptidoglycan transglycosylase RlpA |
| RA | 724,034 | A→C | V52G (GTC→GGC) | kdpA ← | potassium‑transporting ATPase subunit KdpA |
| RA | 788,865 | +G | coding (380/1473 nt) | modF ← | molybdate ABC transporter ATP‑binding protein ModF |
| RA | 859,589 | A→G | A164A (GCA→GCG) | fsa → | fructose‑6‑phosphate aldolase |
| RA | 923,620 | A→G | V344V (GTT→GTC) | cydC ← | cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC |
| RA | 945,384 | (T)5→4 | coding (261/591 nt) | ycaK → | NAD(P)H oxidoreductase |
| RA | 966,040 | A→G | D399G (GAT→GGT) | ycaQ → | winged helix DNA‑binding protein YcaQ |
| RA | 1,015,913 | T→G | T155P (ACG→CCG) | sulA ← | cell division inhibitor SulA |
| RA | 1,035,547 | A→G | I266V (ATC→GTC) | appB → | cytochrome d ubiquinol oxidase subunit II |
| RA | 1,036,585 | A→G | G171G (GGA→GGG) | appA → | bifunctional acid phosphatase/4‑phytase |
| RA | 1,041,277 | T→C | intergenic (‑18/+28) | gfcE ← / ← gfcD | polysaccharide export protein/YjbH domain‑containing protein |
| RA | 1,060,660 | T→C | L390P (CTC→CCC) | yccE → | YccE family protein |
| RA | 1,103,672 | C→T | T242T (ACG→ACA) | mdoC ← | glucans biosynthesis protein MdoC |
| RA | 1,188,709 | (T)5→4 | coding (521/1107 nt) | mnmA ← | tRNA 2‑thiouridine(34) synthase MnmA |
| RA | 1,268,640 | A→G | L226L (TTA→TTG) | chaC → | glutathione‑specific gamma‑glutamylcyclotransferase |
| RA | 1,312,468 | T→C | T69A (ACG→GCG) | trpB ← | tryptophan synthase subunit beta |
| RA | 1,314,400 | C→T | A414A (GCG→GCA) | trpD ← | bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD |
| RA | 1,444,183 | T→G | Q475P (CAG→CCG) | tynA ← | primary‑amine oxidase |
| RA | 1,624,590 | T→C | D194G (GAC→GGC) | ydfI ← | mannitol dehydrogenase family protein |
| RA | 1,632,424 | (A)7→6 | intergenic (‑58/+21) | BW25113_RS08135 ← / ← BW25113_RS25620 | hypothetical protein/hypothetical protein |
| RA | 1,678,263 | C→T | R375R (CGC→CGT) | rstB → | two‑component system sensor histidine kinase RstB |
| RA | 1,679,189 | A→G | N225S (AAC→AGC) | tus → | DNA replication terminus site‑binding protein |
| RA | 1,695,442 | T→G | F77V (TTT→GTT) | malY → | bifunctional maltose regulon transcriptional repressor/cystathionine beta‑lyase MalY |
| RA | 1,747,881 | A→C | G97G (GGT→GGG) | ydhV ← | aldehyde ferredoxin oxidoreductase |
| RA | 1,776,120 | A→G | I157V (ATT→GTT) | ydiS → | FAD‑dependent oxidoreductase |
| RA | 1,806,054 | T→C | S288S (AGT→AGC) | tcyP → | cystine/sulfocysteine:cation symporter |
| RA | 1,809,486 | A→C | T455P (ACT→CCT) | katE → | catalase HPII |
| RA | 1,819,028 | T→C | E56G (GAA→GGA) | ves ← | environmental stress‑induced protein Ves |
| RA | 1,865,194 | A→C | N185H (AAC→CAC) | cdgI → | GGDEF domain‑containing protein |
| RA | 1,919,822 | T→C | F42F (TTT→TTC) | yobB → | carbon‑nitrogen hydrolase family protein |
| RA | 1,948,189 | T→G | V164G (GTG→GGG) | cmoB → | tRNA 5‑methoxyuridine(34)/uridine 5‑oxyacetic acid(34) synthase CmoB |
| RA | 1,976,083 | T→G | A313A (GCA→GCC) | araH ← | arabinose ABC transporter permease AraH |
| RA | 1,976,582 | T→G | Y147S (TAC→TCC) | araH ← | arabinose ABC transporter permease AraH |
| RA | 1,980,983 | T→G | intergenic (+74/+5) | ftnB → / ← yecJ | non‑heme ferritin‑like protein/DUF2766 domain‑containing protein |
| RA | 1,982,130 | G→A | intergenic (+104/‑67) | yecR → / → ftnA | YecR‑like lipofamily protein/non‑heme ferritin |
| RA | 2,000,655 | A→G | E340G (GAA→GGA) | amyA → | alpha‑amylase |
| RA | 2,009,052 | A→G | D231G (GAC→GGC) | fliG → | flagellar motor switch protein FliG |
| RA | 2,052,030 | T→C | D433G (GAT→GGT) | yeeO ← | toxic metabolite efflux MATE transporter YeeO |
| RA | 2,065,124 | T→G | G35G (GGT→GGG) | agn43 → | autotransporter adhesin Ag43 |
| RA | 2,069,352 | A→C | T365P (ACA→CCA) | BW25113_RS10450 → | hypothetical protein |
| RA | 2,071,153 | G→C | G35A (GGC→GCC) | cbtA → | type IV toxin‑antitoxin system cytoskeleton‑binding toxin CbtA |
| RA | 2,141,824 | T→C | S224P (TCA→CCA) | yegD → | molecular chaperone |
| RA | 2,154,426 | A→G | I854V (ATC→GTC) | mdtC → | multidrug efflux RND transporter permease subunit MdtC |
| RA | 2,211,818 | A→C | C73W (TGT→TGG) | yehY ← | glycine betaine ABC transporter permease YehY |
| RA | 2,221,311 | A→G | pseudogene (927/1436 nt) | mdtQ ← | multidrug resistance outer membrane protein MdtQ |
| RA | 2,237,080 | G→C | R18G (CGA→GGA) | folE ← | GTP cyclohydrolase I FolE |
| RA | 2,243,084 | A→G | L5P (CTC→CCC) | yeiE ← | DNA‑binding transcriptional regulator YeiE |
| RA | 2,247,045 | C→T | A194T (GCA→ACA) | nupX ← | NupC/NupG family nucleoside CNT transporter |
| RA | 2,253,834 | A→G | I352I (ATT→ATC) | fruA ← | PTS fructose transporter subunit IIBC |
| RA | 2,322,128 | (C)5→4 | coding (1149/1650 nt) | yfaQ ← | YfaQ family protein |
| RA | 2,378,215 | A→G | D329D (GAT→GAC) | yfbK ← | VWA domain‑containing protein |
| MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
| RA | 2,418,201 | A→G | L171P (CTG→CCG) | hisM ← | ABC transporter permease |
| RA | 2,424,458 | A→G | intergenic (‑216/+43) | cvpA ← / ← dedD | colicin V production protein/cell division protein DedD |
| RA | 2,483,956 | A→G | S492P (TCA→CCA) | oxc ← | oxalyl‑CoA decarboxylase |
| RA | 2,547,539 | A→G | S335P (TCC→CCC) | eutR ← | HTH‑type transcriptional regulator EutR |
| RA | 2,561,055 | A→G | S138P (TCC→CCC) | eutH ← | ethanolamine utilization protein EutH |
| RA | 2,676,053 | T→G | T18P (ACC→CCC) | yphG ← | DUF5107 domain‑containing protein |
| RA | 2,756,916 | T→C | K533E (AAG→GAG) | abpA ← | anti‑bacteriophage protein AbpA |
| RA | 2,777,187 | T→C | pseudogene (1184/1374 nt) | BW25113_RS25705 ← | DUF5507 domain‑containing protein |
| RA | 2,786,008 | T→G | G459G (GGT→GGG) | gabD → | NADP‑dependent succinate‑semialdehyde dehydrogenase |
| RA | 2,831,745 | A→G | I293I (ATT→ATC) | ascG ← | DNA‑binding transcriptional regulator AscG |
| RA | 2,884,026 | T→C | D411G (GAC→GGC) | cysJ ← | NADPH‑dependent assimilatory sulfite reductase flavoprotein subunit |
| RA | 2,926,085 | A→C | G96G (GGT→GGG) | fucO ← | lactaldehyde reductase |
| RA | 2,960,176 | G→A | R540W (CGG→TGG) | ptsP ← | phosphoenolpyruvate‑‑protein phosphotransferase |
| RA | 2,974,914 | Δ1 bp | coding (628/1419 nt) | araE ← | arabinose‑proton symporter AraE |
| RA | 2,984,282 | (C)6→7 | pseudogene (370/490 nt) | BW25113_RS14825 → | hypothetical protein |
| RA | 3,000,345 | (A)5→4 | coding (722/1188 nt) | ygeW → | knotted carbamoyltransferase YgeW |
| RA | 3,027,998 | T→C | E179G (GAA→GGA) | lysS ← | lysine‑‑tRNA ligase |
| RA | 3,104,251 | T→G | T79P (ACC→CCC) | yghD ← | GspM family type II secretion system protein YghD |
| RA | 3,111,922 | T→C | N184D (AAT→GAT) | sslE ← | lipoprotein metalloprotease SslE |
| RA | 3,246,701 | A→G | I291I (ATT→ATC) | yhaJ ← | DNA‑binding transcriptional regulator YhaJ |
| RA | 3,263,514 | T→C | intergenic (+553/+61) | yhaC → / ← rnpB | YhaC family protein/RNase P RNA component class A |
| RA | 3,332,009 | A→G | V200A (GTC→GCC) | mlaE ← | lipid asymmetry maintenance ABC transporter permease subunit MlaE |
| RA | 3,351,627 | C→T | L1182L (CTG→TTG) | gltB → | glutamate synthase large subunit |
| RA | 3,473,413 | A→G | M185T (ATG→ACG) | kefB ← | glutathione‑regulated potassium‑efflux system protein KefB |
| RA | 3,572,235 | A→G | intergenic (‑149/+75) | gntR ← / ← yhhW | gluconate operon transcriptional repressor GntR/quercetin 2,3‑dioxygenase |
| RA | 3,633,239 | (T)8→7 | intergenic (‑159/‑232) | uspB ← / → uspA | universal stress protein UspB/universal stress protein UspA |
| RA | 3,639,274 | T→C | V177A (GTC→GCC) | rlmJ → | 23S rRNA (adenine(2030)‑N(6))‑methyltransferase |
| RA | 3,747,593 | C→G | A66P (GCC→CCC) | yiaW ← | DUF3302 domain‑containing protein |
| RA | 3,829,452 | T→G | intergenic (‑163/‑130) | yicJ ← / → BW25113_RS18990 | glycoside‑pentoside‑hexuronide family transporter/tRNA‑Sec |
| RA | 3,876,284 | T→C | D269G (GAT→GGT) | dnaA ← | chromosomal replication initiator protein DnaA |
| RA | 3,937,289 | A→G | noncoding (226/2904 nt) | BW25113_RS19530 → | 23S ribosomal RNA |
| RA | 3,969,741 | C→T | A35V (GCG→GTG) | wzxE → | lipid III flippase WzxE |
| RA | 4,009,285 | T→C | E82G (GAG→GGG) | ysgA ← | dienelactone hydrolase family protein |
| RA | 4,029,029 | A→T | noncoding (139/1542 nt) | BW25113_RS19980 → | 16S ribosomal RNA |
| RA | 4,058,644 | Δ1 bp | coding (483/1404 nt) | yihO ← | MFS transporter |
| RA | 4,062,410 | G→T | P76Q (CCG→CAG) | yihQ ← | sulfoquinovosidase |
| RA | 4,091,145 | C→T | G136G (GGC→GGT) | sodA → | superoxide dismutase [Mn] |
| RA | 4,113,018 | G→A | R84C (CGC→TGC) | ftsN ← | cell division protein FtsN |
| RA | 4,130,531 | A→G | I540T (ATC→ACC) | ptsP ← | phosphoenolpyruvate‑‑protein phosphotransferase |
| RA | 4,192,005 | A→G | E51G (GAA→GGA) | zraS → | two‑component system sensor histidine kinase ZraS |
| RA | 4,320,763 | T→C | S149P (TCG→CCG) | proP → | glycine betaine/L‑proline transporter ProP |
| RA | 4,389,340 | A→G | E91G (GAA→GGA) | miaA → | tRNA (adenosine(37)‑N6)‑dimethylallyltransferase MiaA |
| RA | 4,401,268 | T→G | G50G (GGT→GGG) | yjfK → | YjfK family protein |
| RA | 4,464,092 | (C)6→5 | coding (152/594 nt) | bdcR → | TetR/AcrR family transcriptional regulator |
| RA | 4,498,429 | T→G | R2S (AGA→AGC) | BW25113_RS22240 ← | IS30‑like element IS30 family transposase |
| RA | 4,507,805 | T→C | E83G (GAA→GGA) | fecI ← | RNA polymerase sigma factor FecI |
| RA | 4,524,810 | A→G | pseudogene (203/1241 nt) | yjhR → | helicase YjhR |
| RA | 4,589,054 | T→G | T69P (ACC→CCC) | opgB ← | phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_CP009273 | 233697 | 233749 | 53 | 2 [1] | [0] 2 | BW25113_RS01085/BW25113_RS01090 | tRNA‑Asp/lipoprotein |
| * | * | ÷ | NZ_CP009273 | 356981 | 357571 | 591 | 3 [0] | [1] 2 | lacA | galactoside O‑acetyltransferase |
| * | * | ÷ | NZ_CP009273 | 711065 | 711127 | 63 | 2 [1] | [1] 2 | BW25113_RS03560 | lipoprotein |
| * | * | ÷ | NZ_CP009273 | 902977 | 903032 | 56 | 3 [1] | [1] 2 | ybjT | SDR family oxidoreductase |
| * | * | ÷ | NZ_CP009273 | 993855 | 993868 | 14 | 2 [1] | [0] 2 | [elfA] | [elfA] |
| * | * | ÷ | NZ_CP009273 | 1212157 | 1212166 | 10 | 2 [0] | [1] 3 | ariR/BW25113_RS06060 | biofilm/acid‑resistance regulator AriR/hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 2988511 | 2988573 | 63 | 2 [1] | [1] 2 | BW25113_RS14850/BW25113_RS26010 | response regulator transcription factor/hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 360104 = | 31 (1.200) | 35 (1.360) | 24/246 | 0.1 | 53.0% | 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 = | 16 (0.620) | 7 (0.310) | 6/214 | 1.3 | 36.0% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | 1205075 = | 11 (0.490) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | 4532499 = | 6 (0.230) | 3 (0.130) | 3/228 | 2.1 | 27.8% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 10 (0.420) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 6 (0.230) | 8 (0.330) | 8/228 | 1.1 | 50.7% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 10 (0.420) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||