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 | freq | annotation | gene | description |
| RA | 10,620 | A→T | 5.2% | intergenic (‑126/+23) | satP ← / ← yaaW | succinate‑acetate transporter/UPF0174 family protein |
| RA | 53,379 | T→C | 5.1% | E13G (GAG→GGG) | pdxA ← | 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 299,984 | T→G | 8.9% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 318,651 | T→A | 5.1% | intergenic (‑84/+25) | rclB ← / ← rclA | reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family |
| RA | 318,652 | T→A | 5.0% | intergenic (‑85/+24) | rclB ← / ← rclA | reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family |
| RA | 318,654 | G→A | 5.0% | intergenic (‑87/+22) | rclB ← / ← rclA | reactive chlorine species (RCS) stress resistance periplasmic protein/reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family |
| RA | 349,717 | T→C | 6.9% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 406,656 | G→A | 5.2% | T84T (ACG→ACA) | aroL → | shikimate kinase II |
| RA | 473,057 | A→G | 5.3% | D31G (GAC→GGC) | amtB → | ammonium transporter |
| RA | 481,225 | T→G | 5.2% | intergenic (‑517/+29) | tomB ← / ← acrB | Hha toxicity attenuator; conjugation‑related protein/multidrug efflux system protein |
| RA | 495,026 | A→T | 5.9% | intergenic (+16/‑94) | recR → / → htpG | gap repair protein/protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent; heat‑shock protein; ATPase |
| RA | 495,027 | T→G | 5.9% | intergenic (+17/‑93) | recR → / → htpG | gap repair protein/protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent; heat‑shock protein; ATPase |
| RA | 495,028 | C→A | 5.8% | intergenic (+18/‑92) | recR → / → htpG | gap repair protein/protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent; heat‑shock protein; ATPase |
| RA | 495,029 | A→T | 5.8% | intergenic (+19/‑91) | recR → / → htpG | gap repair protein/protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent; heat‑shock protein; ATPase |
| RA | 574,494 | A→G | 7.6% | intergenic (+155/+35) | quuD → / ← nmpC | DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 574,495 | A→T | 7.6% | intergenic (+156/+34) | quuD → / ← nmpC | DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 574,496 | C→T | 7.6% | intergenic (+157/+33) | quuD → / ← nmpC | DLP12 prophage; putative antitermination protein/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 644,042 | C→T | 5.0% | intergenic (‑75/+155) | rnk ← / ← rna | regulator of nucleoside diphosphate kinase/ribonuclease I |
| RA | 645,069 | G→A | 5.3% | intergenic (‑66/+48) | rna ← / ← citT | ribonuclease I/citrate/succinate antiporter; citrate carrier |
| RA | 645,070 | G→A | 5.2% | intergenic (‑67/+47) | rna ← / ← citT | ribonuclease I/citrate/succinate antiporter; citrate carrier |
| RA | 645,073 | T→C | 5.1% | intergenic (‑70/+44) | rna ← / ← citT | ribonuclease I/citrate/succinate antiporter; citrate carrier |
| RA | 645,074 | T→C | 5.1% | intergenic (‑71/+43) | rna ← / ← citT | ribonuclease I/citrate/succinate antiporter; citrate carrier |
| RA | 659,204 | C→T | 8.5% | intergenic (+54/+47) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,205 | A→T | 9.2% | intergenic (+55/+46) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,206 | A→T | 9.3% | intergenic (+56/+45) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,207 | A→G | 9.4% | intergenic (+57/+44) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 710,170 | C→T | 6.4% | intergenic (+54/+30) | chiQ → / ← fur | chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor |
| RA | 710,173 | A→G | 6.2% | intergenic (+57/+27) | chiQ → / ← fur | chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor |
| RA | 729,376 | G→T | 6.0% | intergenic (+36/‑207) | ybfA → / → rhsC | DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 729,377 | A→T | 6.0% | intergenic (+37/‑206) | ybfA → / → rhsC | DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 729,378 | A→T | 6.0% | intergenic (+38/‑205) | ybfA → / → rhsC | DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 729,379 | A→C | 5.6% | intergenic (+39/‑204) | ybfA → / → rhsC | DUF2517 family protein/Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 760,167 | G→A | 5.8% | A488T (GCT→ACT) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 770,187 | T→C | 5.2% | L737P (CTG→CCG) | mngB → | alpha‑mannosidase |
| RA | 781,238 | T→A | 6.2% | intergenic (+16/‑131) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,254 | A→T | 8.1% | intergenic (+32/‑115) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 781,269 | C→T | 5.2% | intergenic (+47/‑100) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 802,888 | C→T | 6.5% | I334I (ATC→ATT) | ybhI → | putative DASS family tricarboxylate or dicarboxylate transporter |
| RA | 838,930 | T→A | 8.5% | Y93F (TAT→TTT) | ybiX ← | Fe(II)‑dependent oxygenase superfamily protein |
| RA | 852,372 | A→G | 5.4% | F76L (TTC→CTC) | opgE ← | OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 933,500 | G→A | 5.1% | G93S (GGT→AGT) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 1,011,009 | C→T | 5.2% | A349V (GCC→GTC) | uup → | replication regulatory ABC‑F family DNA‑binding ATPase |
| RA | 1,099,456 | C→A | 6.9% | S193Y (TCT→TAT) | ycdX → | alkaline phosphatase |
| RA | 1,147,690 | G→A | 5.7% | A24T (GCA→ACA) ‡ | plsX → | putative phosphate acyltransferase |
| RA | 1,147,691 | C→T | 5.7% | A24V (GCA→GTA) ‡ | plsX → | putative phosphate acyltransferase |
| RA | 1,147,692 | A→G | 5.7% | A24A (GCA→GCG) ‡ | plsX → | putative phosphate acyltransferase |
| RA | 1,147,693 | T→C | 5.5% | L25L (TTG→CTG) | plsX → | putative phosphate acyltransferase |
| RA | 1,457,532 | A→C | 5.0% | V12V (GTA→GTC) | paaF → | 2,3‑dehydroadipyl‑CoA hydratase |
| RA | 1,466,336 | C→G | 5.3% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,345 | T→C | 6.9% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,515,338 | G→T | 7.5% | G193* (GGA→TGA) | ydcV → | putative ABC transporter permease |
| RA | 1,688,120 | C→T | 6.1% | V86V (GTG→GTA) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,708,709 | T→A | 5.8% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,792,242 | T→A | 5.0% | intergenic (‑222/+25) | ydiV ← / ← nlpC | anti‑FlhD4C2 factor, inactive EAL family phosphodiesterase/putative C40 clan peptidase lipoprotein |
| RA | 1,807,316 | G→A | 7.8% | intergenic (+17/‑84) | pfkB → / → ydiZ | 6‑phosphofructokinase II/uncharacterized protein |
| RA | 1,807,317 | C→T | 7.8% | intergenic (+18/‑83) | pfkB → / → ydiZ | 6‑phosphofructokinase II/uncharacterized protein |
| RA | 1,807,318 | A→G | 7.9% | intergenic (+19/‑82) | pfkB → / → ydiZ | 6‑phosphofructokinase II/uncharacterized protein |
| RA | 1,864,763 | A→T | 7.5% | intergenic (+29/+19) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,864,768 | T→C | 6.8% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,009,731 | A→G | 5.8% | intergenic (+19/‑90) | yedF → / → yedK | putative TusA family sulfurtransferase/DUF159 family protein |
| RA | 2,009,732 | C→G | 5.7% | intergenic (+20/‑89) | yedF → / → yedK | putative TusA family sulfurtransferase/DUF159 family protein |
| RA | 2,009,733 | C→T | 5.7% | intergenic (+21/‑88) | yedF → / → yedK | putative TusA family sulfurtransferase/DUF159 family protein |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,079,004 | G→C | 10.6% | intergenic (+73/+28) | yoeF → / ← yeeX | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein |
| RA | 2,104,190 | T→C | 8.4% | Y107C (TAT→TGT) | wbbK ← | lipopolysaccharide biosynthesis protein |
| RA | 2,129,974 | A→G | 5.8% | F302S (TTT→TCT) | wcaD ← | putative colanic acid polymerase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,210,853 | A→G | 5.3% | pseudogene (1754/2001 nt) | yehQ → | pseudogene |
| RA | 2,292,341 | G→A | 5.7% | Q24* (CAG→TAG) | ccmH ← | heme lyase, CcmH subunit |
| RA | 2,304,649 | C→T | 14.3% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,988 | T→C | 9.4% | intergenic (+595/+120) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,013 | A→G | 5.4% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,440,295 | A→T | 7.2% | intergenic (‑175/+90) | yfcJ ← / ← fabB | putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,440,296 | T→G | 7.0% | intergenic (‑176/+89) | yfcJ ← / ← fabB | putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,440,297 | C→A | 7.0% | intergenic (‑177/+88) | yfcJ ← / ← fabB | putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,440,298 | A→T | 7.1% | intergenic (‑178/+87) | yfcJ ← / ← fabB | putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,460,614 | C→T | 7.1% | intergenic (‑145/+36) | fadI ← / ← yfcZ | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein |
| RA | 2,460,618 | C→T | 6.8% | intergenic (‑149/+32) | fadI ← / ← yfcZ | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein |
| RA | 2,460,619 | A→T | 6.8% | intergenic (‑150/+31) | fadI ← / ← yfcZ | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein |
| RA | 2,460,620 | A→G | 6.8% | intergenic (‑151/+30) | fadI ← / ← yfcZ | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein |
| RA | 2,460,624 | A→G | 6.7% | intergenic (‑155/+26) | fadI ← / ← yfcZ | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein |
| RA | 2,470,427 | C→A | 26.8% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,503,518 | G→T | 8.4% | A323D (GCC→GAC) ‡ | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,503,519 | C→T | 7.8% | A323T (GCC→ACC) ‡ | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,503,522 | A→G | 8.1% | Y322H (TAT→CAT) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,503,523 | A→C | 9.4% | R321R (CGT→CGG) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,521,344 | C→T | 7.5% | intergenic (+16/+249) | lysV → / ← xapR | tRNA‑Lys/transcriptional activator of xapAB |
| RA | 2,521,346 | A→T | 7.2% | intergenic (+18/+247) | lysV → / ← xapR | tRNA‑Lys/transcriptional activator of xapAB |
| RA | 2,521,348 | A→G | 7.6% | intergenic (+20/+245) | lysV → / ← xapR | tRNA‑Lys/transcriptional activator of xapAB |
| RA | 2,561,206 | A→T | 5.2% | intergenic (+308/‑162) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,622,348:1 | +A | 5.2% | coding (115/639 nt) | purN → | phosphoribosylglycinamide formyltransferase 1 |
| RA | 2,622,354 | Δ1 bp | 5.4% | coding (121/639 nt) | purN → | phosphoribosylglycinamide formyltransferase 1 |
| RA | 2,662,505 | G→T | 5.9% | intergenic (‑374/+78) | iscR ← / ← trmJ | isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 2,663,482 | A→C | 7.1% | K14T (AAG→ACG) | suhB → | inositol monophosphatase |
| RA | 2,666,972 | C→T | 5.6% | W292* (TGG→TAG) | hcaT ← | putative 3‑phenylpropionic transporter |
| RA | 2,666,978 | A→G | 5.5% | L290S (TTG→TCG) ‡ | hcaT ← | putative 3‑phenylpropionic transporter |
| RA | 2,666,979 | A→T | 5.3% | L290M (TTG→ATG) ‡ | hcaT ← | putative 3‑phenylpropionic transporter |
| RA | 2,666,980 | C→T | 5.3% | A289A (GCG→GCA) | hcaT ← | putative 3‑phenylpropionic transporter |
| RA | 2,666,986 | A→G | 5.5% | T287T (ACT→ACC) | hcaT ← | putative 3‑phenylpropionic transporter |
| RA | 2,726,043 | G→T | 5.8% | intergenic (‑297/+26) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,726,044 | T→G | 5.5% | intergenic (‑298/+25) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,726,045 | C→A | 5.9% | intergenic (‑299/+24) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,726,046 | A→C | 5.7% | intergenic (‑300/+23) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,817,916 | T→G | 6.0% | intergenic (‑56/+143) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,145 | T→C | 6.4% | intergenic (‑10/+53) | argZ ← / ← argY | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,149 | T→C | 6.6% | intergenic (‑14/+49) | argZ ← / ← argY | tRNA‑Arg/tRNA‑Arg |
| RA | 2,907,998 | A→T | 7.2% | intergenic (‑57/+31) | eno ← / ← pyrG | enolase/CTP synthetase |
| RA | 2,980,742 | A→G | 7.1% | intergenic (‑107/+22) | ygeA ← / ← araE | Asp/Glu_racemase family protein/arabinose transporter |
| RA | 2,980,744 | A→T | 7.1% | intergenic (‑109/+20) | ygeA ← / ← araE | Asp/Glu_racemase family protein/arabinose transporter |
| RA | 2,980,746 | C→T | 7.3% | intergenic (‑111/+18) | ygeA ← / ← araE | Asp/Glu_racemase family protein/arabinose transporter |
| RA | 2,987,103 | C→T | 9.1% | intergenic (+27/‑433) | yqeG → / → yqeH | putative transporter/putative LuxR family transcriptional regulator |
| RA | 2,987,104 | T→A | 10.1% | intergenic (+28/‑432) | yqeG → / → yqeH | putative transporter/putative LuxR family transcriptional regulator |
| RA | 2,987,105 | A→G | 9.4% | intergenic (+29/‑431) | yqeG → / → yqeH | putative transporter/putative LuxR family transcriptional regulator |
| RA | 3,042,403 | A→T | 5.7% | intergenic (+110/+86) | ygfZ → / ← yqfA | iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein |
| RA | 3,042,404 | A→C | 5.8% | intergenic (+111/+85) | ygfZ → / ← yqfA | iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein |
| RA | 3,042,410 | T→G | 5.7% | intergenic (+117/+79) | ygfZ → / ← yqfA | iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein |
| RA | 3,042,411 | C→A | 5.7% | intergenic (+118/+78) | ygfZ → / ← yqfA | iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein |
| RA | 3,042,417 | G→T | 5.6% | intergenic (+124/+72) | ygfZ → / ← yqfA | iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein |
| RA | 3,042,418 | A→T | 5.5% | intergenic (+125/+71) | ygfZ → / ← yqfA | iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein |
| RA | 3,046,050 | T→G | 11.1% | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase/glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex |
| RA | 3,092,842 | G→A | 5.8% | intergenic (+14/‑95) | gshB → / → yqgE | glutathione synthetase/uncharacterized protein |
| RA | 3,156,590 | C→A | 6.8% | intergenic (+72/‑33) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,156,591 | T→G | 6.8% | intergenic (+73/‑32) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,183,345:1 | +T | 5.0% | intergenic (+22/+468) | zupT → / ← ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| RA | 3,239,609 | T→G | 11.9% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,239,610 | C→G | 7.8% | intergenic (+65/‑334) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,239,611 | C→A | 7.6% | intergenic (+66/‑333) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,269,956 | T→C | 6.2% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,269,969 | A→C | 5.7% | intergenic (+367/+247) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,080 | C→T | 5.5% | intergenic (+478/+136) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,081 | G→T | 5.5% | intergenic (+479/+135) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,082 | A→C | 9.6% | intergenic (+480/+134) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,083 | A→G | 5.3% | intergenic (+481/+133) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,143 | C→T | 5.1% | intergenic (+541/+73) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,283,652 | C→T | 5.7% | D170D (GAC→GAT) | kbaY → | tagatose 6‑phosphate aldolase 1, kbaY subunit |
| RA | 3,313,207 | G→A | 5.1% | intergenic (‑29/+135) | rbfA ← / ← infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| RA | 3,313,208 | T→A | 5.2% | intergenic (‑30/+134) | rbfA ← / ← infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| RA | 3,313,209 | T→C | 5.2% | intergenic (‑31/+133) | rbfA ← / ← infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| RA | 3,324,952 | A→G | 5.6% | intergenic (‑41/+49) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,955 | A→G | 5.7% | intergenic (‑44/+46) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,956 | C→T | 5.7% | intergenic (‑45/+45) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,959 | C→T | 5.8% | intergenic (‑48/+42) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,328,182 | A→T | 6.9% | intergenic (+99/+57) | yhbY → / ← greA | RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor |
| RA | 3,328,183 | T→A | 6.9% | intergenic (+100/+56) | yhbY → / ← greA | RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor |
| RA | 3,328,184 | A→T | 6.6% | intergenic (+101/+55) | yhbY → / ← greA | RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor |
| RA | 3,392,189 | T→G | 5.2% | intergenic (‑161/+269) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,392,190 | T→C | 5.4% | intergenic (‑162/+268) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,504,855 | T→G | 9.0% | intergenic (+72/+80) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,507,076 | G→C | 5.5% | L87L (CTC→CTG) | yhfT ← | inner membrane protein |
| RA | 3,557,462 | C→A | 5.6% | E206D (GAG→GAT) | rtcB ← | RNA‑splicing ligase |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,569,442 | C→T | 5.2% | E626E (GAG→GAA) | glgX ← | glycogen debranching enzyme |
| RA | 3,578,609 | T→G | 5.3% | I40L (ATT→CTT) | gntR ← | d‑gluconate inducible gluconate regulon transcriptional repressor |
| RA | 3,608,721 | A→C | 9.9% | intergenic (+72/+30) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,642,358 | T→A | 5.4% | intergenic (+27/+22) | dtpB → / ← rsmJ | dipeptide and tripeptide permease B/16S rRNA m(2)G1516 methyltransferase, SAM‑dependent |
| RA | 3,781,126 | G→T | 7.3% | intergenic (+109/‑89) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,132 | C→G | 7.4% | intergenic (+115/‑83) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,133 | C→A | 6.8% | intergenic (+116/‑82) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,781,138 | A→C | 10.0% | intergenic (+121/‑77) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,959,457 | T→G | 8.0% | intergenic (+12/+75) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 4,008,408 | A→G | 5.9% | intergenic (+31/+31) | rhtC → / ← rhtB | threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump |
| RA | 4,008,409 | A→C | 5.9% | intergenic (+32/+30) | rhtC → / ← rhtB | threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump |
| RA | 4,008,415 | T→A | 6.9% | intergenic (+38/+24) | rhtC → / ← rhtB | threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump |
| RA | 4,008,416 | T→A | 6.2% | intergenic (+39/+23) | rhtC → / ← rhtB | threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump |
| RA | 4,008,422 | G→T | 5.7% | intergenic (+45/+17) | rhtC → / ← rhtB | threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump |
| RA | 4,008,423 | C→T | 6.4% | intergenic (+46/+16) | rhtC → / ← rhtB | threonine efflux pump/homoserine, homoserine lactone and S‑methyl‑methionine efflux pump |
| RA | 4,070,410 | C→A | 6.5% | intergenic (‑9/+105) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,070,413 | T→G | 6.8% | intergenic (‑12/+102) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,183,669 | G→T | 77.1% | G809C (GGT→TGT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,185,540 | C→T | 14.2% | P64L (CCG→CTG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,244,626 | T→A | 7.3% | K150N (AAA→AAT) | malF ← | maltose transporter subunit |
| RA | 4,295,964 | A→G | 5.0% | intergenic (+170/+472) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,295,965 | A→C | 6.2% | intergenic (+171/+471) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,060 | C→T | 42.5% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,397 | T→C | 6.3% | intergenic (+603/+39) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,366,854 | T→G | 7.5% | intergenic (‑81/+37) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,366,855 | C→A | 7.2% | intergenic (‑82/+36) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,370,148 | C→T | 5.1% | G89S (GGC→AGC) | yjeH ← | putative transporter |
| RA | 4,387,993 | T→C | 5.2% | S460G (AGT→GGT) | mscM ← | mechanosensitive channel protein, miniconductance |
| RA | 4,406,129 | T→C | 100% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,422,895 | C→G | 5.1% | A17G (GCC→GGC) | ulaE → | L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 4,457,196 | A→G | 5.4% | intergenic (+38/+118) | mpl → / ← yjgA | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase/ribosome‑associated UPF0307 family protein |
| RA | 4,503,229 | G→A | 7.3% | P68L (CCT→CTT) | insG ← | IS4 transposase |
| RA | 4,517,430 | C→G | 5.0% | W96C (TGG→TGC) | fecR ← | anti‑sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| RA | 4,517,556 | T→G | 5.0% | E54D (GAA→GAC) ‡ | fecR ← | anti‑sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| RA | 4,517,557 | T→A | 5.0% | E54V (GAA→GTA) ‡ | fecR ← | anti‑sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| RA | 4,614,321 | A→G | 8.5% | intergenic (+61/+359) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,614,580 | G→A | 8.8% | intergenic (+320/+100) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,621,023 | G→A | 8.5% | L47L (CTG→CTA) | deoD → | purine nucleoside phosphorylase 1; nicotinamide 1‑beta‑D‑riboside phosphorylase |
| JC JC | 4,640,551 | IS1 (–) +9 bp | 100% | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 773010 | 774219 | 1210 | 61 [60] | [60] 61 | [cydA]–[cydX] | [cydA],cydB,[cydX] |
| * | * | ÷ | NC_000913 | 1037687 | 1039353 | 1667 | 62 [57] | [60] 61 | cbdA–[cbdB] | cbdA,[cbdB] |
| * | * | ÷ | NC_000913 | 2403928 | 2404637 | 710 | 67 [59] | [60] 61 | nuoB–[nuoA] | nuoB,[nuoA] |
| * | * | ÷ | NC_000913 | 3423758–3424234 | 3424544–3424238 | 5–787 | 62 [55] | [59] 62 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 16653 | NA (NA) | 3 (0.020) | 3/264 | NT | NA | noncoding (1267/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 16691 | NA (NA) | noncoding (1305/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 316201 | NA (NA) | 4 (0.030) | 3/260 | NT | NA | noncoding (973/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316220 | NA (NA) | noncoding (992/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 111 (0.780) | 39 (0.310) | 23/246 | NT | 31.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 75 (0.600) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 110 (0.770) | 47 (0.370) | 24/246 | NT | 35.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 75 (0.600) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 104 (0.750) | 48/270 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 2726200 = | NA (NA) | 8 (0.060) | 4/266 | NT | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||