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 | 24,776 | T→C | F796L (TTT→CTT) | ileS → | isoleucine‑‑tRNA ligase |
RA | 86,112 | A→G | L161L (TTA→TTG) | ilvI → | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
RA | 119,595 | C→T | A105A (GCC→GCT) | ampE → | protein AmpE |
RA | 132,519 | A→G | N302S (AAC→AGC) | acnB → | hypothetical protein |
RA | 164,090 | A→G | E662E (GAA→GAG) | hrpB → | putative ATP‑dependent RNA helicase HrpB |
RA | 184,723 | G→A | A116V (GCC→GTC) | yaeI ← | phosphodiesterase YaeI |
RA | 186,485 | G→A | A722A (GCC→GCT) | glnD ← | PII uridylyltransferase/uridylyl removing enzyme |
RA | 218,835 | (A)8→7 | intergenic (‑60/+52) | proS ← / ← trmO | proline‑‑tRNA ligase/tRNA m(6)t(6)A37 methyltransferase |
MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
RA | 296,675 | A→G | V141A (GTC→GCC) | intF ← | CP4‑6 prophage; putative phage integrase |
RA | 341,276 | A→G | D51G (GAC→GGC) | yahJ → | putative deaminase with metallo‑dependent hydrolase domain |
RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
RA | 405,536 | G→T | P37T (CCC→ACC) | proC ← | pyrroline‑5‑carboxylate reductase |
RA | 455,208 | A→G | T26A (ACC→GCC) | tig → | trigger factor |
RA | 472,742 | (G)6→7 | coding (145/339 nt) | glnK → | nitrogen regulator GlnK |
RA | 485,897 | G→A | G46D (GGT→GAT) | acrR → | DNA‑binding transcriptional repressor AcrR |
RA | 486,482 | C→T | intergenic (+74/‑54) | acrR → / → mscK | DNA‑binding transcriptional repressor AcrR/potassium dependent, small conductance mechanosensitive channel |
RA | 513,820 | A→G | L415L (TTA→TTG) | ybaT → | putative transporter YbaT |
RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
RA | 663,851 | A→G | I38T (ATC→ACC) | dacA ← | D‑alanyl‑D‑alanine carboxypeptidase DacA |
RA | 705,972 | (T)9→8 | intergenic (+82/‑121) | nagE → / → glnS | N‑acetylglucosamine specific PTS enzyme IIABC component/glutamine‑‑tRNA ligase |
RA | 723,528 | (T)8→7 | coding (887/2685 nt) | kdpD ← | sensory histidine kinase KdpD |
RA | 778,251 | T→C | V171A (GTT→GCT) | tolB → | Tol‑Pal system periplasmic protein TolB |
RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
RA | 915,468 | C→T | A194T (GCT→ACT) | aqpZ ← | water channel AqpZ |
RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
RA | 936,936 | G→C | G1238A (GGT→GCT) | ftsK → | cell division DNA translocase FtsK |
RA | 972,000 | A→G | E83E (GAA→GAG) | ycbJ → | putative phosphotransferase YcbJ |
RA | 983,040 | A→G | intergenic (+146/‑35) | ldtD → / → ycbK | L,D‑transpeptidase LdtD/DUF882 domain‑containing protein YcbK |
RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
RA | 1,014,334 | A→G | H359R (CAC→CGC) | pqiB → | intermembrane transport protein PqiB |
RA | 1,097,580 | (G)7→8 | noncoding (73/88 nt) | serX ← | tRNA‑Ser |
RA | 1,109,534 | A→G | D67G (GAC→GGC) | opgG → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein G |
RA | 1,120,815 | A→G | G47G (GGT→GGC) | bssS ← | regulator of biofilm formation |
RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
RA | 1,195,426 | C→T | P102S (CCG→TCG) | icd → | isocitrate dehydrogenase |
RA | 1,207,903 | T→C | W135R (TGG→CGG) | ycfK → | e14 prophage; protein StfP |
RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
RA | 1,289,331 | (A)7→6 | coding (87/906 nt) | rssA → | putative patatin‑like phospholipase RssA |
RA | 1,328,639 | T→C | G158G (GGA→GGG) | yciK ← | putative oxidoreductase |
RA | 1,333,620 | G→A | G858D (GGC→GAC) | topA → | DNA topoisomerase 1 |
RA | 1,399,985 | (C)7→8 | coding (252/516 nt) | ogt ← | methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
RA | 1,415,063 | T→C | D775G (GAC→GGC) | recE ← | Rac prophage; exonuclease VIII, ds DNA exonuclease, 5' ‑‑> 3' specific |
RA | 1,437,183 | T→C | noncoding (63/109 nt) | micC → | small regulatory RNA MicC |
RA | 1,463,955 | A→G | A139A (GCA→GCG) | paaX → | DNA‑binding transcriptional repressor PaaX |
RA | 1,489,590 | T→C | R453R (CGT→CGC) | aldA → | aldehyde dehydrogenase A |
RA | 1,491,159 | A→G | G86G (GGA→GGG) | cybB → | cytochrome b561 |
RA | 1,515,300 | A→G | Y180C (TAC→TGC) | ydcV → | putative ABC transporter membrane subunit YdcV |
RA | 1,516,041 | C→T | A155V (GCC→GTC) | patD → | gamma‑aminobutyraldehyde dehydrogenase |
RA | 1,538,930 | A→G | F1221L (TTC→CTC) | narZ ← | nitrate reductase Z subunit alpha |
RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
RA | 1,566,171 | C→T | G324S (GGT→AGT) | dosC ← | diguanylate cyclase DosC |
RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
RA | 1,683,424 | A→G | E181E (GAA→GAG) | rstB → | sensory histidine kinase RstB |
RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
RA | 1,731,215 | A→G | H710R (CAT→CGT) | lhr → | putative ATP‑dependent helicase Lhr |
RA | 1,825,986 | C→T | R313H (CGC→CAC) | astE ← | succinylglutamate desuccinylase |
RA | 1,833,212 | T→C | V262A (GTC→GCC) | xthA → | exodeoxyribonuclease III |
RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
RA | 1,875,056 | (C)6→7 | coding (521/822 nt) | nimR ← | DNA‑binding transcriptional repressor NimR |
JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
RA | 2,049,679 | T→C | L1581P (CTG→CCG) | yeeJ → | inverse autotransporter adhesin |
RA | 2,117,185 | T→C | E407G (GAG→GGG) | wcaK ← | putative colanic acid biosynthesis pyruvyl transferase |
RA | 2,129,520 | T→C | N44S (AAC→AGC) | wcaE ← | putative colanic acid biosynthesis glycosyl transferase |
RA | 2,168,165 | T→C | T48A (ACC→GCC) | yegR ← | uncharacterized protein YegR |
RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
RA | 2,184,736 | C→G | G189A (GGT→GCT) | thiM ← | hydroxyethylthiazole kinase |
RA | 2,197,918 | T→C | intergenic (+620/‑2361) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
RA | 2,206,031 | G→A | D113N (GAT→AAT) | yehM → | putative YehN |
RA | 2,286,291 | (A)5→4 | intergenic (+4/+99) | proL → / ← yejO | tRNA‑Pro/adhesin‑like autotransporter YejO |
RA | 2,325,984 | T→C | I410T (ATC→ACC) | atoE → | short chain fatty acid transporter |
RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
RA | 2,477,624 | T→C | E2E (GAA→GAG) | dsdC ← | DNA‑binding transcriptional dual regulator DsdC |
RA | 2,480,487 | T→C | V429A (GTG→GCG) | dsdA → | D‑serine ammonia‑lyase |
RA | 2,511,445 | T→C | intergenic (+118/+23) | ypeC → / ← mntH | DUF2502 domain‑containing protein YpeC/Mn(2(+))/Fe(2(+)): H(+) symporter MntH |
RA | 2,526,738 | T→C | E40G (GAA→GGA) | yfeR ← | putative LysR‑type DNA‑binding transcriptional regulator YfeR |
RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
RA | 2,575,000 | (T)6→5 | coding (4/702 nt) coding (458/480 nt) |
eutQ ← eutP ← |
putative ethanolamine utilization protein EutQ putative ethanolamine utilization protein EutP with nucleoside triphosphate hydrolase domain |
RA | 2,586,334 | A→G | T202A (ACC→GCC) | narQ → | sensory histidine kinase NarQ |
RA | 2,608,676 | T→C | F64L (TTT→CTT) | hyfG → | hydrogenase 4 catalytic subunit HyfG |
RA | 2,631,085 | T→C | H484R (CAC→CGC) | guaA ← | GMP synthetase |
RA | 2,638,026 | (C)6→7 | coding (627/1179 nt) | bamB ← | outer membrane protein assembly factor BamB |
RA | 2,657,686 | A→G | V417A (GTG→GCG) | hscA ← | iron‑sulfur cluster biosynthesis chaperone HscA |
RA | 2,686,857 | T→C | G341G (GGT→GGC) | hmp → | nitric oxide dioxygenase |
RA | 2,785,204 | (A)8→7 | intergenic (‑193/+558) | ypjC ← / ← ileY | DUF5507 domain‑containing protein YpjC/tRNA‑Ile |
RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
RA | 2,814,290 | T→C | E148E (GAA→GAG) | luxS ← | S‑ribosylhomocysteine lyase |
RA | 2,816,416 | C→T | A8A (GCG→GCA) | gshA ← | glutamate‑‑cysteine ligase |
RA | 2,826,722 | G→A | G111S (GGC→AGC) | srlE → | sorbitol‑specific PTS enzyme IIBC1 component |
RA | 2,855,509 | T→C | V391A (GTG→GCG) | fhlA → | DNA‑binding transcriptional activator FhlA |
MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
RA | 2,955,650 | T→C | E118E (GAA→GAG) | recB ← | exodeoxyribonuclease V subunit RecB |
RA | 2,964,144 | T→C | T12A (ACG→GCG) | ppdA ← | conserved protein PpdA |
RA | 3,020,895 | T→C | V119A (GTC→GCC) | ygfM → | putative oxidoreductase |
RA | 3,063,906 | T→C | V307A (GTC→GCC) | argK → | methylmalonyl‑CoA mutase‑interacting GTPase YgfD |
RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
RA | 3,073,784 | T→C | intergenic (‑93/+192) | epd ← / ← yggC | D‑erythrose‑4‑phosphate dehydrogenase/P‑loop NTPase domain‑containing protein YggC |
RA | 3,094,703 | (C)5→4 | coding (378/981 nt) | yggR ← | Type II/IV secretion system family protein |
RA | 3,146,132 | T→C | T44A (ACT→GCT) | hybO ← | hydrogenase 2 small subunit |
RA | 3,197,632 | A→G | G670G (GGT→GGC) | glnE ← | fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase |
RA | 3,255,685 | A→G | C323R (TGT→CGT) | cyuA ← | putative L‑cysteine desulfidase CyuA |
RA | 3,257,356 | (T)5→4 | coding (655/1332 nt) | cyuP ← | putative D/L‑serine transporter |
RA | 3,348,279 | (C)6→7 | intergenic (+41/‑173) | npr → / → yrbL | phosphorelay protein Npr/protein kinase‑like domain‑containing protein YrbL |
RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
RA | 3,448,581 | T→C | K60R (AAG→AGG) | rpmC ← | 50S ribosomal subunit protein L29 |
RA | 3,517,260 | T→A | D16V (GAT→GTT) | damX ← | cell division protein DamX |
RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
RA | 3,649,516 | A→G | L194L (TTA→TTG) | arsB → | arsenite/antimonite:H(+) antiporter |
RA | 3,690,933 | G→A | P559S (CCT→TCT) | bcsB ← | cellulose synthase periplasmic subunit |
RA | 3,696,493 | T→C | G12G (GGT→GGC) | bcsE → | c‑di‑GMP‑binding protein BcsE |
RA | 3,755,238 | G→A | A425V (GCG→GTG) | aldB ← | aldehyde dehydrogenase B |
RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
RA | 3,836,468 | T→C | intergenic (+152/‑485) | selC → / → setC | tRNA‑Sec/putative arabinose exporter |
RA | 3,847,201 | A→G | intergenic (‑34/+104) | uhpT ← / ← uhpC | hexose‑6‑phosphate:phosphate antiporter/inner membrane protein sensing glucose‑6‑phosphate |
RA | 3,853,966 | A→G | L15L (TTA→TTG) | emrD → | multidrug efflux pump EmrD |
RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
RA | 3,926,259 | A→G | L66P (CTT→CCT) | mioC ← | flavoprotein MioC |
RA | 3,935,073 | (A)6→5 | coding (1296/1506 nt) | rbsA → | ribose ABC transporter ATP binding subunit |
RA | 3,994,558 | A→G | T13A (ACT→GCT) | yifL → | putative lipoprotein YifL |
RA | 4,011,856 | A→G | T261A (ACG→GCG) | bioP → | biotin transporter |
RA | 4,032,131 | T→C | V324A (GTC→GCC) | pepQ → | Xaa‑Pro dipeptidase |
RA | 4,075,441 | A→G | Q258R (CAG→CGG) | yihW → | putative DNA‑binding transcriptional regulator YihW |
RA | 4,124,105 | A→G | L118L (TTG→CTG) | cytR ← | DNA‑binding transcriptional repressor CytR |
RA | 4,185,871 | C→T | D174D (GAC→GAT) | rpoC → | RNA polymerase subunit beta' |
RA | 4,188,352 | G→A | A1001A (GCG→GCA) | rpoC → | RNA polymerase subunit beta' |
RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
RA | 4,440,531 | C→T | E229K (GAA→AAA) | ytfL ← | putative inner membrane protein |
RA | 4,442,332 | C→T | intergenic (‑156/‑50) | msrA ← / → tamA | methionine sulfoxide reductase A/translocation and assembly module subunit TamA |
RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
RA | 4,487,894 | G→A | A193T (GCT→ACT) | lptG → | lipopolysaccharide transport system protein LptG |
RA | 4,514,021 | G→A | A96A (GCC→GCT) | fecB ← | ferric citrate ABC transporter periplasmic binding protein |
RA | 4,572,630 | (T)6→7 | coding (217/1518 nt) | yjiT → | putative uncharacterized protein YjiT |
RA | 4,606,094 | (G)8→7 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
JC | 4,606,330 | (G)8→11 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
RA | 4,610,149 | T→C | F246L (TTC→CTC) | prfC → | peptide chain release factor RF3 |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NC_000913 | 270648–271294 | 271484–271385 | 92–837 | 14 [13] | [12] 14 | insI‑1 | IS30 transposase |
* | * | ÷ | NC_000913 | 3423777–3424234 | 3424527–3424239 | 6–751 | 15 [13] | [13] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
* | * | ÷ | NC_000913 | 3762360–3764072 | 3765194–3764077 | 6–2835 | 14 [11] | [13] 14 | rhsA | rhs element protein RhsA |
* | * | ÷ | NC_000913 | 3765317–3765410 | 3765545–3765414 | 5–229 | 15 [12] | [13] 17 | rhsA | rhs element protein RhsA |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | 374921 = | NA (NA) | 23 (0.630) | 16/190 | 1.1 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
* | ? | NC_000913 | 374922 = | NA (NA) | 11 (0.280) | 9/202 | 2.6 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
* | ? | NC_000913 | = 374963 | NA (NA) | 24 (0.650) | 17/190 | 1.0 | NA | noncoding (33/34 nt) | other | REP31a |
? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
* | ? | NC_000913 | 375124 = | NA (NA) | 10 (0.270) | 7/192 | 3.0 | NA | intergenic (+243/‑335) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
* | ? | NC_000913 | 375327 = | NA (NA) | 20 (0.390) | 13/262 | 2.5 | NA | intergenic (+446/‑132) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
? | NC_000913 | 377328 = | NA (NA) | intergenic (+17/+207) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
* | ? | NC_000913 | 1207790 = | 9 (0.170) | 55 (1.160) | 39/244 | 0.2 | 87.3% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
? | NC_000913 | 1209619 = | 8 (0.170) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
* | ? | NC_000913 | = 1207805 | 9 (0.170) | 26 (0.550) | 22/244 | 1.1 | 76.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
? | NC_000913 | = 1209602 | 8 (0.170) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
* | ? | NC_000913 | = 1299498 | 0 (0.000) | 69 (1.330) | 47/268 | 0.1 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
* | ? | NC_000913 | 3363001 = | 81 (1.510) | 85 (1.600) | 53/274 | 0.1 | 67.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
? | NC_000913 | 3766087 = | 2 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
* | ? | NC_000913 | = 3653230 | NA (NA) | 67 (1.250) | 47/276 | 0.1 | 94.4% | noncoding (1/1195 nt) | IS5 | repeat region |
? | NC_000913 | = 3766089 | 4 (0.070) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA |