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 | 45,367 | C→T | S396S (AGC→AGT) | fixC → | FAD‑dependent oxidoreductase |
| RA | 49,765 | C→T | intergenic (+134/‑58) | kefC → / → folA | glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase |
| RA | 49,898 | G→A | A26T (GCC→ACC) | folA → | 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 | 96,834 | A→C | Q235P (CAA→CCA) | murG → | undecaprenyldiphospho‑muramoylpentapeptide beta‑N‑acetylglucosaminyltransferase |
| RA | 100,067 | A→G | G142G (GGA→GGG) | ftsQ → | cell division protein FtsQ |
| RA | 123,341 | T→A | L387Q (CTG→CAG) | aceF → | pyruvate dehydrogenase complex dihydrolipoyllysine‑residue acetyltransferase |
| RA | 183,409 | A→G | F577L (TTT→CTT) | glnD ← | bifunctional uridylyltransferase/uridylyl‑removing protein GlnD |
| RA | 193,289 | A→G | H86R (CAC→CGC) | rseP → | sigma E protease regulator RseP |
| RA | 232,843 | T→A | I97N (ATC→AAC) | dnaQ → | DNA polymerase III subunit epsilon |
| RA | 251,770 | T→C | E145G (GAA→GGA) | pepD ← | cytosol nonspecific dipeptidase |
| RA | 345,822 | A→T | T34S (ACC→TCC) | prpC → | 2‑methylcitrate synthase |
| RA | 362,870 | G→T | Q9H (CAG→CAT) | mhpA → | bifunctional 3‑(3‑hydroxy‑phenyl)propionate/3‑hydroxycinnamic acid hydroxylase |
| RA | 412,148 | G→A | V87V (GTC→GTT) | sbcD ← | exonuclease subunit SbcD |
| RA | 443,081 | C→T | L27L (CTG→CTA) | cyoE ← | heme o synthase |
| RA | 449,442 | A→G | V61A (GTC→GCC) | yajG ← | lipoprotein |
| RA | 547,771 | T→C | T94A (ACT→GCT) | purK ← | 5‑(carboxyamino)imidazole ribonucleotide synthase |
| RA | 633,831 | C→T | A67T (GCT→ACT) | dsbG ← | thiol:disulfide interchange protein DsbG |
| RA | 640,333 | A→C | W43G (TGG→GGG) | rna ← | ribonuclease I |
| RA | 753,637 | A→G | N165D (AAT→GAT) | sdhB → | succinate dehydrogenase iron‑sulfur subunit SdhB |
| RA | 798,635 | T→C | G431G (GGT→GGC) | ybhI → | anion permease |
| RA | 918,237 | T→A | N14K (AAT→AAA) | yljB → | protein YljB |
| RA | 1,006,907 | T→C | D496D (GAT→GAC) | uup → | ABC transporter ATP‑binding protein |
| RA | 1,017,704 | C→A | A549S (GCC→TCC) | yccS ← | YccS family putative transporter |
| RA | 1,069,819 | T→G | L41R (CTG→CGG) | rutR → | HTH‑type transcriptional regulator RutR |
| RA | 1,100,664 | A→T | D83V (GAT→GTT) | csgC → | curli assembly chaperone CsgC |
| RA | 1,121,190 | G→A | G58D (GGC→GAC) | rimJ → | ribosomal protein S5‑alanine N‑acetyltransferase |
| RA | 1,134,272 | A→G | T147A (ACC→GCC) | flgK → | flagellar hook‑associated protein FlgK |
| RA | 1,199,864 | G→A | pseudogene (239/246 nt) pseudogene (8/1137 nt) |
BW25113_RS26105 → BW25113_RS05965 → |
helix‑turn‑helix domain‑containing protein terminase large subunit |
| RA | 1,213,874 | Δ1 bp | coding (1091/1524 nt) | pdeG → | cyclic diguanylate phosphodiesterase |
| RA | 1,280,272 | G→A | A405T (GCA→ACA) | narH → | nitrate reductase subunit beta |
| RA | 1,314,400 | C→T | A414A (GCG→GCA) | trpD ← | bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD |
| RA | 1,350,506 | G→T | R288S (CGT→AGT) | sapA ← | peptide ABC transporter substrate‑binding protein SapA |
| RA | 1,386,326 | C→T | R27C (CGC→TGC) | pgrR → | DNA‑binding transcriptional regulator PgrR |
| RA | 1,395,746 | C→T | L95L (CTG→CTA) | abgT ← | p‑aminobenzoyl‑glutamate transporter |
| RA | 1,505,565 | A→C | N436H (AAC→CAC) | ydcR → | PLP‑dependent aminotransferase family protein |
| RA | 1,524,293 | A→G | intergenic (+98/‑105) | BW25113_RS07645 → / → BW25113_RS26145 | RHS repeat protein/hypothetical protein |
| RA | 1,541,514 | T→C | intergenic (‑88/‑144) | yddG ← / → fdnG | aromatic amino acid efflux DMT transporter YddG/formate dehydrogenase‑N subunit alpha |
| RA | 1,549,065 | C→T | A288T (GCG→ACG) | maeA ← | malate dehydrogenase |
| RA | 1,550,159 | C→T | R21H (CGC→CAC) | sra ← | stationary‑phase‑induced ribosome‑associated protein |
| RA | 1,581,105 | A→G | V296A (GTC→GCC) | ydeQ ← | fimbrial protein |
| RA | 1,603,097 | A→C | G61G (GGT→GGG) | yneE ← | bestrophin family protein |
| RA | 1,620,338 | A→G | S434P (TCA→CCA) | dcp ← | peptidyl‑dipeptidase Dcp |
| RA | 1,635,187 | T→C | P42P (CCT→CCC) | ynfU → | putative zinc‑binding protein YnfU |
| RA | 1,718,009 | A→G | E544E (GAA→GAG) | ydhK → | FUSC family protein |
| RA | 1,744,804 | T→C | E156G (GAG→GGG) | ydhX ← | 4Fe‑4S dicluster domain‑containing protein |
| RA | 1,752,926 | C→T | Q19Q (CAG→CAA) | ldtE ← | L,D‑transpeptidase LdtE |
| RA | 1,785,565 | T→C | *238* (TAA→TGA) | ydiV ← | anti‑FlhDC factor |
| RA | 1,820,976 | C→T | A69T (GCG→ACG) | astE ← | succinylglutamate desuccinylase |
| RA | 1,891,283 | A→G | D32G (GAT→GGT) | sdaA → | L‑serine ammonia‑lyase |
| RA | 1,913,346 | T→G | V527G (GTG→GGG) | yebT → | lipid‑binding membrane homeostasis protein YebT |
| RA | 1,927,446 | A→G | V472V (GTT→GTC) | edd ← | phosphogluconate dehydratase |
| RA | 1,977,975 | C→T | E192E (GAG→GAA) | araG ← | arabinose ABC transporter ATP‑binding protein AraG |
| RA | 2,014,277 | A→G | E237G (GAA→GGA) | fliM → | flagellar motor switch protein FliM |
| RA | 2,018,781 | A→G | intergenic (+87/‑211) | yodD → / → yedP | peroxide/acid resistance protein YodD/mannosyl‑3‑phosphoglycerate phosphatase‑related protein |
| RA | 2,134,005 | T→C | Q363Q (CAA→CAG) | asmA ← | outer membrane assembly protein AsmA |
| RA | 2,370,899 | A→T | V58D (GTC→GAC) | menH ← | 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase |
| MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
| RA | 2,400,959 | A→C | intergenic (‑839/‑81) | lrhA ← / → alaA | transcriptional regulator LrhA/alanine transaminase AlaA |
| RA | 2,441,796 | A→C | W42G (TGG→GGG) | prmB ← | 50S ribosomal protein L3 N(5)‑glutamine methyltransferase |
| RA | 2,451,709 | G→T | S310R (AGC→AGA) | fadJ ← | fatty acid oxidation complex subunit alpha FadJ |
| RA | 2,482,405 | A→G | D81D (GAT→GAC) | yfdE ← | CoA:oxalate CoA‑transferase |
| RA | 2,484,113 | A→G | S439S (TCT→TCC) | oxc ← | oxalyl‑CoA decarboxylase |
| RA | 2,497,341 | (C)5→4 | coding (624/2496 nt) | ptsP ← | phosphoenolpyruvate‑‑protein phosphotransferase |
| RA | 2,521,249 | A→C | K315N (AAA→AAC) | yfeH → | bile acid:sodium symporter |
| RA | 2,590,869 | Δ1 bp | coding (109/714 nt) | purC ← | phosphoribosylaminoimidazolesuccinocarboxamide synthase |
| RA | 2,595,868 | T→C | L231S (TTG→TCG) | hyfB → | hydrogenase 4 subunit B |
| RA | 2,625,832 | T→C | Q21Q (CAA→CAG) | guaA ← | glutamine‑hydrolyzing GMP synthase |
| RA | 2,636,307 | A→G | intergenic (‑104/+181) | rodZ ← / ← rlmN | cytoskeleton protein RodZ/bifunctional tRNA (adenosine(37)‑C2)‑methyltransferase TrmG/ribosomal RNA large subunit methyltransferase RlmN |
| RA | 2,705,165 | G→A | A463T (GCC→ACC) | nadB → | L‑aspartate oxidase |
| RA | 2,718,722 | A→G | L128L (CTT→CTC) | kgtP ← | alpha‑ketoglutarate permease |
| RA | 2,718,745 | T→G | T121P (ACG→CCG) | kgtP ← | alpha‑ketoglutarate permease |
| RA | 2,724,669 | T→G | intergenic (‑153/+290) | BW25113_RS13535 ← / ← clpB | 16S ribosomal RNA/ATP‑dependent chaperone ClpB |
| RA | 2,724,674 | T→C | intergenic (‑158/+285) | BW25113_RS13535 ← / ← clpB | 16S ribosomal RNA/ATP‑dependent chaperone ClpB |
| RA | 2,781,609 | T→C | pseudogene (1854/2253 nt) | BW25113_RS26005 → | alpha‑amylase family glycosyl hydrolase |
| RA | 2,897,407 | A→C | intergenic (+674/+699) | ygcE → / ← queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 2,901,362 | A→G | intergenic (‑62/+26) | eno ← / ← pyrG | phosphopyruvate hydratase/CTP synthase (glutamine hydrolyzing) |
| RA | 2,923,200 | A→G | D89G (GAT→GGT) | sdaB → | L‑serine ammonia‑lyase II |
| RA | 2,982,682 | (A)8→7 | coding (20/483 nt) | BW25113_RS14815 → | hypothetical protein |
| RA | 2,985,850 | A→G | D133G (GAT→GGT) | ygeH → | HilA family transcriptional regulator YgeH |
| RA | 2,999,490 | T→C | intergenic (‑345/‑134) | ygeV ← / → ygeW | sigma‑54‑dependent Fis family transcriptional regulator/knotted carbamoyltransferase YgeW |
| RA | 3,050,507 | A→G | intergenic (‑199/+30) | ibsC ← / ← serA | type I toxin‑antitoxin system toxin IbsC/phosphoglycerate dehydrogenase |
| RA | 3,063,057 | A→T | I37N (ATC→AAC) | mscS ← | small‑conductance mechanosensitive channel MscS |
| RA | 3,085,483 | A→T | I83F (ATC→TTC) | gshB → | glutathione synthase |
| RA | 3,168,157 | A→T | I200N (ATC→AAC) | parE ← | DNA topoisomerase IV subunit B |
| RA | 3,223,174 | A→T | I310F (ATC→TTC) | ygjK → | alpha‑glucosidase |
| RA | 3,286,821 | C→T | A21A (GCC→GCT) | lpoA → | penicillin‑binding protein activator LpoA |
| RA | 3,310,402 | T→A | I162F (ATC→TTC) | nusA ← | transcription termination factor NusA |
| RA | 3,366,821 | T→C | I39V (ATC→GTC) | nanA ← | N‑acetylneuraminate lyase |
| RA | 3,394,698 | T→C | intergenic (‑252/+53) | mreB ← / ← csrD | rod shape‑determining protein MreB/RNase E specificity factor CsrD |
| RA | 3,403,270 | A→G | E281G (GAA→GGA) | prmA → | 50S ribosomal protein L11 methyltransferase |
| RA | 3,429,447 | T→G | G294G (GGT→GGG) | rsmB → | 16S rRNA (cytosine(967)‑C(5))‑methyltransferase RsmB |
| RA | 3,452,746 | G→T | G350V (GGC→GTC) | gspE → | type II secretion system ATPase GspE |
| RA | 3,467,417 | A→G | pseudogene (24/468 nt) | rpsG ← | 30S ribosomal protein S7 |
| RA | 3,501,576 | T→C | E125G (GAG→GGG) | php ← | phosphotriesterase‑related protein |
| RA | 3,539,325 | C→T | L115L (CTG→TTG) | nfuA → | Fe‑S biogenesis protein NfuA |
| RA | 3,540,121 | C→T | G68G (GGC→GGT) | gntT → | gluconate transporter |
| RA | 3,543,436 | T→C | intergenic (‑7/+3) | malQ ← / ← malP | 4‑alpha‑glucanotransferase/maltodextrin phosphorylase |
| RA | 3,595,866 | A→G | I81T (ATT→ACT) | ftsE ← | cell division ATP‑binding protein FtsE |
| RA | 3,660,392 | Δ1 bp | coding (549/1401 nt) | gadA ← | glutamate decarboxylase |
| RA | 3,710,430 | C→T | A175V (GCG→GTG) | yiaD → | OmpA family lipoprotein |
| RA | 3,750,235 | T→C | E318G (GAA→GGA) | yiaY ← | L‑threonine dehydrogenase |
| RA | 3,781,002 | A→G | T269A (ACG→GCG) | envC → | murein hydrolase activator EnvC |
| RA | 3,805,353 | T→C | E189E (GAA→GAG) | radC ← | DNA repair protein RadC |
| RA | 3,816,198 | C→T | L147L (CTG→TTG) | spoT → | bifunctional GTP diphosphokinase/guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,858,886 | T→C | T250A (ACC→GCC) | yidE ← | putative transporter |
| RA | 3,913,243 | A→C | V174G (GTC→GGC) | atpH ← | F0F1 ATP synthase subunit delta |
| RA | 3,976,044 | (C)8→9 | noncoding (79/87 nt) | BW25113_RS19725 → | tRNA‑Leu |
| RA | 3,994,324 | A→G | V31V (GTT→GTC) | yigE ← | phosphodiester glycosidase family protein |
| RA | 3,994,419 | T→C | intergenic (‑3/‑159) | yigE ← / → ysgD | phosphodiester glycosidase family protein/protein YsgD |
| RA | 4,041,206 | G→A | G294D (GGC→GAC) | polA → | DNA polymerase I |
| RA | 4,062,410 | G→T | P76Q (CCG→CAG) | yihQ ← | sulfoquinovosidase |
| RA | 4,078,866 | C→T | S106N (AGC→AAC) | fdnG ← | formate dehydrogenase‑N subunit alpha |
| RA | 4,078,948 | C→A | E79* (GAA→TAA) | fdnG ← | formate dehydrogenase‑N subunit alpha |
| RA | 4,222,007 | A→C | G385G (GGT→GGG) | lysC ← | lysine‑sensitive aspartokinase 3 |
| RA | 4,272,855 | A→G | L50P (CTC→CCC) | espX5 ← | T3SS effector pentapeptide repeat protein EspX5 |
| RA | 4,469,838 | C→T | L98F (CTT→TTT) | yjgN → | YjgN family protein |
| RA | 4,516,576 | A→G | Y44H (TAT→CAT) | sgcR ← | DeoR/GlpR family DNA‑binding transcription regulator |
| RA | 4,585,319 | Δ1 bp | coding (350/915 nt) | lgoR ← | GntR family transcriptional regulator |
| RA | 4,616,195 | A→G | E156G (GAA→GGA) | radA → | DNA repair protein RadA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_CP009273 | 356954 | 357592 | 639 | 8 [7] | [5] 8 | lacA | lacA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 360104 = | 37 (0.880) | 52 (1.240) | 35/236 | 0.1 | 58.4% | 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 = | 6 (0.140) | 22 (0.610) | 18/204 | 0.7 | 78.3% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | 1205075 = | 7 (0.190) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1203261 | 6 (0.140) | 15 (0.410) | 13/204 | 1.2 | 71.1% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | = 1205058 | 7 (0.190) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | 1390700 = | NA (NA) | 16 (0.380) | 14/236 | 1.4 | 41.0% | coding (332/981 nt) | BW25113_RS06980 | IS5‑like element IS5 family transposase |
| ? | NZ_CP009273 | 1422137 = | 23 (0.550) | coding (847/981 nt) | BW25113_RS07180 | IS5‑like element ISKpn26 family transposase | |||||
| * | ? | NZ_CP009273 | 4532499 = | 21 (0.500) | 8 (0.210) | 8/218 | 2.2 | 23.7% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 32 (0.830) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||