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 | 6,892 | A→G | V356V (GTT→GTC) | yaaJ ← | putative transporter YaaJ |
| RA | 14,155 | C→T | intergenic (+76/‑13) | dnaK → / → dnaJ | chaperone protein DnaK/chaperone protein DnaJ |
| RA | 42,683 | +A | coding (281/771 nt) | fixA → | putative electron transfer flavoprotein FixA |
| RA | 48,757 | T→C | V330A (GTG→GCG) | kefC → | K(+) : H(+) antiporter KefC |
| RA | 70,787 | T→C | F134S (TTT→TCT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 88,680 | A→G | N218S (AAC→AGC) | cra → | DNA‑binding transcriptional dual regulator Cra |
| RA | 101,917 | A→G | T385A (ACC→GCC) | murC → | UDP‑N‑acetylmuramate‑‑L‑alanine ligase |
| RA | 166,936 | C→T | A736V (GCC→GTC) | mrcB → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| RA | 185,773 | A→G | L59L (TTG→CTG) | dapD ← | tetrahydrodipicolinate succinylase |
| RA | 205,802 | A→G | D226G (GAC→GGC) | dnaE → | DNA polymerase III subunit alpha |
| RA | 226,175 | C→T | noncoding (417/2904 nt) | rrlH → | 23S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 269,495 | C→T | G230S (GGC→AGC) | perR ← | putative transcriptional regulator PerR |
| RA | 275,399 | C→T | G25G (GGC→GGT) | mmuP → | S‑methyl‑L‑methionine transporter |
| RA | 285,560 | G→A | D56N (GAC→AAC) | yagG → | putative D‑xylonate transporter YagG |
| RA | 297,941 | T→C | Q262Q (CAA→CAG) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 321,564 | (G)7→8 | intergenic (+483/‑44) | rclR → / → ykgE | DNA‑binding transcriptional activator RclR/putative lactate utilization oxidoreductase YkgE |
| RA | 359,221 | A→G | L141L (TTA→TTG) | cynT → | carbonic anhydrase 1 |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 404,225 | T→C | W175R (TGG→CGG) | dgcC → | diguanylate cyclase DgcC |
| RA | 422,549 | (C)5→6 | coding (32/1815 nt) | malZ → | maltodextrin glucosidase |
| RA | 453,396 | A→G | G50G (GGT→GGC) | ampG ← | muropeptide:H(+) symporter |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 539,933 | A→G | T263A (ACT→GCT) | allB → | allantoinase |
| RA | 563,278 | C→T | P315S (CCG→TCG) | sfmH → | putative fimbrial adhesin protein SfmH |
| RA | 573,138 | G→A | G19S (GGC→AGC) | ybcO → | DLP12 prophage; putative nuclease YbcO |
| RA | 621,912 | C→T | G93D (GGC→GAC) | fepD ← | ferric enterobactin ABC transporter membrane subunit FebD |
| RA | 645,421 | A→G | V387A (GTG→GCG) | citT ← | citrate:succinate antiporter |
| RA | 646,802 | G→C | G236G (GGC→GGG) | citG ← | triphosphoribosyl‑dephospho‑CoA synthase |
| RA | 648,307 | A→G | V422A (GTG→GCG) | citF ← | citrate lyase alpha subunit |
| RA | 669,834 | (G)6→7 | coding (74/612 nt) | cobC ← | putative adenosylcobalamin phosphatase/alpha‑ribazole phosphatase |
| RA | 671,469 | C→T | G46E (GGA→GAA) | holA ← | DNA polymerase III subunit delta |
| RA | 693,180 | A→G | Y67H (TAT→CAT) | ybeZ ← | PhoH‑like protein |
| RA | 697,498 | Δ1 bp | intergenic (‑365/+15) | metT ← / ← asnB | tRNA‑Met/asparagine synthetase B |
| RA | 701,613 | A→G | V380A (GTA→GCA) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 731,011 | G→A | A477T (GCC→ACC) | rhsC → | rhs element protein RhsC |
| RA | 731,472 | T→G | G630G (GGT→GGG) | rhsC → | rhs element protein RhsC |
| RA | 772,973 | A→G | T506A (ACC→GCC) | cydA → | cytochrome bd‑I ubiquinol oxidase subunit I |
| RA | 796,306 | A→G | I149V (ATT→GTT) | modB → | molybdate ABC transporter membrane subunit |
| RA | 810,576 | (G)5→6 | coding (196/1155 nt) | bioF → | 8‑amino‑7‑oxononanoate synthase |
| RA | 811,441 | C→T | P354L (CCC→CTC) | bioF → | 8‑amino‑7‑oxononanoate synthase |
| RA | 829,819 | (C)6→7 | coding (154/999 nt) | ybhG ← | HlyD_D23 family protein YbhG |
| RA | 834,704 | G→A | R545R (CGG→CGA) | dinG → | ATP‑dependent DNA helicase DinG |
| RA | 879,758 | G→A | G339G (GGG→GGA) | yliI → | aldose sugar dehydrogenase YliI |
| RA | 880,631 | A→G | intergenic (‑151/‑96) | gstB ← / → dacC | glutathione S‑transferase GstB/D‑alanyl‑D‑alanine carboxypeptidase DacC |
| RA | 888,099 | T→C | intergenic (‑42/+35) | rybB ← / ← ybjL | small regulatory RNA RybB/putative transport protein YbjL |
| RA | 889,799 | T→C | E7E (GAA→GAG) | ybjL ← | putative transport protein YbjL |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 913,622 | A→G | F65L (TTC→CTC) | hcp ← | protein S‑nitrosylase |
| RA | 925,899 | (G)7→8 | noncoding (73/88 nt) | serW ← | tRNA‑Ser |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 963,206 | A→G | E404E (GAA→GAG) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 986,679 | Δ1 bp | coding (304/1089 nt) | ompF ← | outer membrane porin F |
| RA | 996,973 | A→G | P180P (CCT→CCC) | ssuE ← | NADPH‑dependent FMN reductase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,016,193 | A→G | F93S (TTC→TCC) | fabA ← | beta‑hydroxyacyl‑acyl carrier protein dehydratase/isomerase |
| RA | 1,041,526 | Δ1 bp | coding (910/1299 nt) | appA → | periplasmic phosphoanhydride phosphatase/multiple inositol‑polyphosphate phosphatase |
| RA | 1,042,626 | T→C | T529A (ACG→GCG) | etk ← | protein‑tyrosine kinase Etk |
| RA | 1,101,784 | A→G | V115A (GTG→GCG) | csgF ← | curli assembly component |
| RA | 1,112,249 | (G)6→7 | coding (1387/2544 nt) | opgH → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H |
| RA | 1,116,136 | A→G | G149G (GGT→GGC) | lpxL ← | lauroyl acyltransferase |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,150,644 | C→T | A306V (GCG→GTG) | fabD → | [acyl‑carrier‑protein] S‑malonyltransferase |
| RA | 1,167,461 | T→C | intergenic (+72/‑138) | ndh → / → ycfJ | NADH:quinone oxidoreductase II/PF05433 family protein YcfJ |
| RA | 1,170,031 | T→C | Y115C (TAC→TGC) | ldtC ← | L,D‑transpeptidase YcfS |
| RA | 1,172,076 | A→G | V630A (GTT→GCT) | mfd ← | transcription‑repair coupling factor |
| RA | 1,181,512 | T→C | T72A (ACG→GCG) | ymfA ← | putative inner membrane protein |
| RA | 1,204,656 | A→G | T163A (ACC→GCC) pseudogene (256/1137 nt) |
ymfN → aaaE → |
e14 prophage; chimeric replication protein/phage terminase YmfN phage terminase |
| RA | 1,211,762 | C→T | C81Y (TGT→TAT) | iraM ← | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,268,947 | A→G | E261E (GAA→GAG) | kdsA → | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase |
| RA | 1,293,347 | C→T | intergenic (‑425/‑180) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| RA | 1,303,286 | A→G | T130A (ACC→GCC) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | 1,322,975 | (A)8→9 | intergenic (‑29/+63) | trpE ← / ← trpL | anthranilate synthase subunit TrpE/trp operon leader peptide |
| RA | 1,327,839 | C→T | T173T (ACG→ACA) | btuR ← | cobinamide/cobalamin adenosyltransferase |
| RA | 1,338,450 | A→G | T874A (ACC→GCC) | acnA → | aconitate hydratase 1 |
| RA | 1,354,439 | G→A | A27V (GCC→GTC) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,357,038 | A→G | S25P (TCT→CCT) | sapA ← | putative periplasmic binding protein SapA |
| RA | 1,357,300 | G→A | intergenic (‑190/+123) | sapA ← / ← ymjA | putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA |
| RA | 1,403,605 | C→T | G321S (GGC→AGC) | abgA ← | p‑aminobenzoyl‑glutamate hydrolase subunit A |
| RA | 1,421,237 | C→T | A40V (GCA→GTA) | ydaU → | Rac prophage; DUF1376 domain‑containing protein YdaU |
| RA | 1,422,337 | G→A | A119T (GCA→ACA) | ydaV → | Rac prophage; putative ATP‑binding protein YdaV |
| RA | 1,448,665 | T→C | Y383H (TAT→CAT) | feaB → | phenylacetaldehyde dehydrogenase |
| RA | 1,459,364 | C→T | A104V (GCA→GTA) | paaH → | 3‑hydroxyadipyl‑CoA dehydrogenase |
| RA | 1,473,518 | G→A | pseudogene (3000/3495 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,485,893 | C→T | R945C (CGC→TGC) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,517,665 | A→G | E6E (GAA→GAG) | ydcY → | DUF2526 domain‑containing protein YdcY |
| RA | 1,523,314 | T→C | L3S (TTA→TCA) | yncE → | PQQ‑like domain‑containing protein YncE |
| RA | 1,541,042 | A→G | Y517H (TAT→CAT) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,544,945 | T→C | N257S (AAC→AGC) | yddK ← | leucine‑rich repeat domain‑containing protein YddK |
| RA | 1,570,826 | G→A | P407L (CCG→CTG) | gadB ← | glutamate decarboxylase B |
| RA | 1,587,884 | A→G | F138S (TTT→TCT) | ydeR ← | putative fimbrial protein YdeR |
| 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 | 1,645,196 | T→C | K27E (AAA→GAA) | hokD ← | Qin prophage; toxic protein HokD |
| RA | 1,660,868 | A→G | I105V (ATC→GTC) | ynfF → | putative selenate reductase YnfF |
| RA | 1,677,388 | A→G | G172G (GGT→GGC) | pntA ← | pyridine nucleotide transhydrogenase subunit alpha |
| RA | 1,679,237 | T→C | Y271H (TAC→CAC) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,682,025 | C→T | G2G (GGG→GGA) | ydgC ← | GlpM family protein |
| RA | 1,684,919 | G→A | A221T (GCC→ACC) | tus → | DNA replication terminus site‑binding protein |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,690,705 | T→C | V285A (GTA→GCA) | ydgA → | conserved protein YdgA |
| RA | 1,695,818 | A→G | V85A (GTG→GCG) | uidA ← | beta‑glucuronidase |
| RA | 1,723,568 | T→C | V483A (GTG→GCG) | ydhK → | putative transporter YdhK |
| RA | 1,772,172 | T→C | F368L (TTC→CTC) | ydiM → | putative exporter YdiM |
| RA | 1,783,669 | T→C | I231I (ATT→ATC) | fadK → | short chain acyl‑CoA synthetase |
| RA | 1,788,399 | T→C | intergenic (+121/‑36) | ppsR → / → aroH | posphoenolpyruvate synthetase regulatory protein/3‑deoxy‑7‑phosphoheptulonate synthase, Trp‑sensitive |
| RA | 1,796,854 | A→G | V364A (GTT→GCT) | pheT ← | phenylalanine‑‑tRNA ligase subunit beta |
| RA | 1,824,706 | T→C | T78A (ACC→GCC) | ves ← | HutD family protein Ves |
| RA | 1,843,762 | A→G | intergenic (+48/+69) | gdhA → / ← ynjI | glutamate dehydrogenase/DUF1266 domain‑containing protein YnjI |
| RA | 1,863,290 | A→G | T174A (ACC→GCC) | gapA → | glyceraldehyde‑3‑phosphate dehydrogenase A |
| RA | 1,871,832 | (G)6→5 | coding (1448/1476 nt) | cdgI → | putative c‑di‑GMP binding protein CdgI |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,881,492 | T→C | G106G (GGA→GGG) | dmlR ← | DNA‑binding transcriptional regulator DmlR |
| RA | 1,886,730 | G→A | D296N (GAT→AAT) | yeaX → | carnitine monooxygenase subunit YeaX |
| RA | 1,898,605 | T→C | V60A (GTA→GCA) | pdeD → | putative c‑di‑GMP phosphodiesterase PdeD |
| RA | 1,920,932 | G→A | R237H (CGT→CAT) | rsmF → | 16S rRNA m(5)C1407 methyltransferase |
| RA | 1,928,983 | T→C | intergenic (‑144/+65) | ptrB ← / ← yebE | oligopeptidase B/conserved inner membrane protein YebE |
| RA | 1,958,713 | T→C | H185R (CAC→CGC) | cutC ← | protein CutC |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
| RA | 2,002,844 | T→C | T255A (ACA→GCA) | fliC ← | flagellar filament structural protein |
| RA | 2,008,870 | T→C | R198R (CGT→CGC) | yedE → | putative selenium transporter YedE |
| RA | 2,012,563 | (G)6→7 | pseudogene (62/279 nt) | intG → | putative defective phage integrase |
| RA | 2,015,611 | T→A | D244E (GAT→GAA) | fliG → | flagellar motor switch protein FliG |
| RA | 2,017,280 | C→T | P243S (CCG→TCG) | fliI → | flagellum‑specific ATP synthase FliI |
| RA | 2,021,709 | T→C | V69A (GTG→GCG) | fliO → | flagellar biosynthesis protein FliO |
| RA | 2,055,057 | A→G | intergenic (+98/‑4) | shiA → / → amn | shikimate:H(+) symporter/AMP nucleosidase |
| RA | 2,072,883 | G→A | A449T (GCG→ACG) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,073,251 | G→A | V571V (GTG→GTA) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,089,255 | T→C | T71A (ACC→GCC) | yoeB ← | ribosome‑dependent mRNA interferase toxin YoeB |
| RA | 2,110,445 | G→A | P192L (CCG→CTG) | rfbA ← | dTDP‑glucose pyrophosphorylase |
| RA | 2,134,865 | G→A | A263V (GCG→GTG) | wzc ← | protein‑tyrosine kinase Wzc |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,175,780 | G→A | A181V (GCC→GTC) | gatZ ← | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatZ |
| RA | 2,185,656 | G→A | G47G (GGC→GGT) | rcnR ← | DNA‑binding transcriptional repressor RcnR |
| RA | 2,198,685 | A→G | intergenic (+1387/‑1594) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,262,306 | G→A | C20C (TGC→TGT) | fruK ← | 1‑phosphofructokinase |
| RA | 2,281,013 | A→G | S128G (AGC→GGC) | radD → | putative DNA repair helicase RadD |
| RA | 2,302,942 | G→A | T24T (ACC→ACT) | napD ← | NapA signal peptide‑binding chaperone NapD |
| RA | 2,327,508 | A→G | G212G (GGT→GGC) | yfaP ← | DUF2135 domain‑containing protein YfaP |
| RA | 2,368,510 | G→A | A158T (GCT→ACT) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,395,029 | T→C | L6L (TTA→TTG) | nuoL ← | NADH:quinone oxidoreductase subunit L |
| RA | 2,399,538 | T→C | T210A (ACG→GCG) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,410,707 | T→C | T216A (ACC→GCC) | yfbS ← | putative transporter YfbS |
| RA | 2,423,045 | G→A | D165D (GAC→GAT) | rpnB ← | recombination‑promoting nuclease RpnB |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,460,937 | T→C | intergenic (‑3/‑369) | yfcZ ← / → fadL | DUF406 domain‑containing protein YfcZ/long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor |
| JC | 2,462,889 | (C)9→12 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,565,398 | A→G | intergenic (+66/+83) | yffS → / ← eutA | CPZ‑55 prophage; uncharacterized protein YffS/reactivating factor for ethanolamine ammonia‑lyase EutBC |
| RA | 2,640,836 | G→A | G323G (GGC→GGT) | ispG ← | (E)‑4‑hydroxy‑3‑methylbut‑2‑enyl‑diphosphate synthase (flavodoxin) |
| RA | 2,673,740 | C→T | P132L (CCG→CTG) | yphA → | putative inner membrane protein |
| RA | 2,680,452 | G→A | A765V (GCC→GTC) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,705,117 | C→T | A65T (GCT→ACT) | lepB ← | signal peptidase I |
| RA | 2,709,225 | C→T | M60I (ATG→ATA) | rseA ← | anti‑sigma factor |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,736,648 | T→C | V168A (GTA→GCA) | bamD → | outer membrane protein assembly factor BamD |
| RA | 2,746,240 | T→C | intergenic (‑55/+194) | rpsP ← / ← ffh | 30S ribosomal subunit protein S16/signal recognition particle protein component |
| RA | 2,769,648 | (C)6→5 | intergenic (+162/‑55) | yfjQ → / → yfjR | CP4‑57 prophage; protein YfjQ/CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| RA | 2,770,799 | (C)5→4 | coding (119/444 nt) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,772,591 | A→G | pseudogene (592/1016 nt) | yfjV ← | CP4‑57 prophage; putative arsenite transporter, N‑terminal fragment |
| RA | 2,772,999 | G→A | pseudogene (184/1016 nt) | yfjV ← | CP4‑57 prophage; putative arsenite transporter, N‑terminal fragment |
| RA | 2,785,204 | (A)8→7 | intergenic (‑193/+558) | ypjC ← / ← ileY | DUF5507 domain‑containing protein YpjC/tRNA‑Ile |
| RA | 2,792,180 | A→G | D303G (GAC→GGC) | gabD → | NADP(+)‑dependent succinate‑semialdehyde dehydrogenase |
| RA | 2,794,731 | T→C | V160A (GTC→GCC) | gabP → | 4‑aminobutyrate:H(+) symporter |
| RA | 2,798,530 | (A)7→6 | intergenic (‑35/‑634) | stpA ← / → alaE | DNA‑binding transcriptional repressor StpA with RNA chaperone activity/L‑alanine exporter |
| RA | 2,804,419 | G→A | M306I (ATG→ATA) | nrdF → | ribonucleoside‑diphosphate reductase 2 subunit beta |
| RA | 2,806,989 | T→C | V327A (GTT→GCT) | proW → | glycine betaine ABC transporter membrane subunit ProW |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,827,717 | A→G | E119G (GAA→GGA) | srlB → | sorbitol‑specific PTS enzyme IIA component |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,890,797 | G→A | P368S (CCG→TCG) | cysJ ← | sulfite reductase, flavoprotein subunit |
| RA | 2,920,941 | C→T | G387D (GGC→GAC) | gudP ← | galactarate/glucarate/glycerate transporter GudP |
| RA | 2,948,307 | T→C | Y235C (TAC→TGC) | amiC ← | N‑acetylmuramoyl‑L‑alanine amidase C |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,960,227 | A→G | R734R (CGT→CGC) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,973,022 | T→C | T281A (ACC→GCC) | lplT ← | lysophospholipid transporter |
| RA | 3,000,976 | T→C | V211A (GTT→GCT) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,001,304 | (G)7→8 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,002,032 | T→C | V563A (GTT→GCT) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,027,153 | A→G | A11A (GCA→GCG) | ghxQ → | guanine/hypoxanthine transporter GhxQ |
| RA | 3,028,806 | (C)5→4 | coding (207/489 nt) | ygfS ← | putative oxidoreductase, 4Fe‑4S ferredoxin‑type subunit |
| RA | 3,041,435 | G→A | M41I (ATG→ATA) | ygfZ → | folate‑binding protein |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,160,896 | T→C | D84G (GAC→GGC) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,171,047 | G→A | P188P (CCG→CCA) | qseC → | sensory histidine kinase QseC |
| RA | 3,181,417 | A→G | M333V (ATG→GTG) | ygiC → | putative enzyme with ATPase activity |
| RA | 3,191,075 | T→C | G148G (GGT→GGC) | yqiI → | putative fimbrial protein YqiI |
| RA | 3,201,476 | C→T | S90S (AGC→AGT) | ygiM → | putative signal transduction protein (SH3 domain) |
| RA | 3,207,365 | C→T | S301S (AGC→AGT) | ttdA → | L(+)‑tartrate dehydratase subunit alpha |
| RA | 3,209,379 | T→C | G452G (GGT→GGC) | ttdT → | L‑tartrate:succinate antiporter |
| RA | 3,213,203 | A→G | I53V (ATT→GTT) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,245,898 | T→C | R225R (CGT→CGC) | exuT → | hexuronate transporter |
| RA | 3,304,813 | (C)7→8 | coding (1005/1245 nt) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,312,089 | T→C | D230G (GAT→GGT) | truB ← | tRNA pseudouridine(55) synthase |
| RA | 3,321,197 | (T)7→6 | coding (417/1626 nt) | yhbX ← | putative hydrolase, inner membrane |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,357,018 | T→C | L765P (CTG→CCG) | gltB → | glutamate synthase subunit GltB |
| RA | 3,358,292 | A→G | T1190A (ACT→GCT) | gltB → | glutamate synthase subunit GltB |
| RA | 3,372,310 | C→T | V89I (GTC→ATC) | nanT ← | N‑acetylneuraminate:H(+) symporter |
| RA | 3,375,895 | (G)6→7 | coding (1027/1368 nt) | dcuD → | putative transporter DcuD |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,406,593 | C→T | A226V (GCG→GTG) | accC → | biotin carboxylase |
| RA | 3,437,397 | C→T | H294Y (CAT→TAT) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,455,545 | A→G | intergenic (‑147/‑33) | gspA ← / → gspC | Type II secretion system protein GspA/Type II secretion system protein GspC |
| RA | 3,472,700 | T→C | N272S (AAC→AGC) | fusA ← | elongation factor G |
| RA | 3,490,338 | A→G | G164G (GGT→GGC) | pabA ← | aminodeoxychorismate synthase subunit 2 |
| RA | 3,491,126 | A→G | V113A (GTT→GCT) | fic ← | putative adenosine monophosphate‑‑protein transferase Fic |
| RA | 3,552,586 | A→G | intergenic (‑113/‑499) | malP ← / → malT | maltodextrin phosphorylase/DNA‑binding transcriptional activator MalT |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,577,042 | A→G | V7A (GTT→GCT) | gntU ← | low‑affinity gluconate transporter |
| RA | 3,588,643 | A→G | L180L (TTG→CTG) | ugpC ← | sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit |
| RA | 3,632,500 | T→C | K31E (AAA→GAA) | yhiJ ← | DUF4049 domain‑containing protein YhiJ |
| RA | 3,650,641 | A→G | E135E (GAA→GAG) | arsC → | arsenate reductase |
| RA | 3,650,680 | (C)7→6 | intergenic (+18/‑611) | arsC → / → yhiS | arsenate reductase/putative uncharacterized protein YhiS |
| RA | 3,660,338 | A→G | A369A (GCA→GCG) | mdtE → | multidrug efflux pump membrane fusion protein MdtE |
| RA | 3,669,830 | A→G | D80G (GAC→GGC) | treF → | cytoplasmic trehalase |
| RA | 3,732,867 | A→G | T223A (ACG→GCG) | xylG → | xylose ABC transporter ATP binding subunit |
| RA | 3,748,407 | A→G | T442A (ACC→GCC) | lyxK → | L‑xylulose kinase |
| RA | 3,787,890 | T→C | G351G (GGT→GGC) | envC → | murein hydrolase activator EnvC |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,822,554 | T→C | V52A (GTT→GCT) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,822,657 | A→G | E86E (GAA→GAG) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,852,535 | T→C | S84G (AGC→GGC) | ilvB ← | acetohydroxy acid synthase I subunit IlvB |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,862,224 | G→A | V83V (GTC→GTT) | glvB ← | putative PTS enzyme II component GlvB |
| RA | 3,879,326 | T→C | N265S (AAC→AGC) | gyrB ← | DNA gyrase subunit B |
| RA | 3,919,120 | G→A | G246G (GGC→GGT) | atpA ← | ATP synthase F1 complex subunit alpha |
| RA | 3,926,512 | A→G | intergenic (‑57/+33) | mioC ← / ← asnC | flavoprotein MioC/DNA‑binding transcriptional dual regulator AsnC |
| RA | 3,948,080 | T→C | intergenic (‑113/‑6) | hdfR ← / → maoP | DNA‑binding transcriptional dual regulator HdfR/macrodomain Ori protein |
| RA | 3,999,973 | T→C | V664A (GTC→GCC) | uvrD → | ssDNA translocase and dsDNA helicase ‑ DNA helicase II |
| RA | 4,030,743 | A→G | F77L (TTC→CTC) | fadB ← | dodecenoyl‑CoA delta‑isomerase, enoyl‑CoA hydratase, 3‑hydroxybutyryl‑CoA epimerase, 3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,037,211 | C→T | noncoding (71/77 nt) | ileT → | tRNA‑Ile |
| RA | 4,050,105 | A→G | intergenic (+98/+28) | spf → / ← yihA | small regulatory RNA Spot 42/GTP‑binding protein YihA |
| RA | 4,070,029 | G→A | P125S (CCG→TCG) | yihR ← | putative aldose 1‑epimerase YihR |
| RA | 4,132,292 | T→C | intergenic (+25/‑324) | metL → / → metF | fused aspartate kinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase |
| RA | 4,160,400 | C→T | D131N (GAC→AAC) | sthA ← | soluble pyridine nucleotide transhydrogenase |
| RA | 4,250,294 | A→G | A247A (GCA→GCG) | malM → | maltose regulon periplasmic protein |
| RA | 4,254,975 | G→A | P498S (CCG→TCG) | plsB ← | glycerol‑3‑phosphate 1‑O‑acyltransferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,321,237 | T→C | E4G (GAA→GGA) | phnH ← | carbon‑phosphorus lyase core complex subunit PhnH |
| RA | 4,328,984 | C→T | S617L (TCG→TTG) | crfC → | clamp‑binding sister replication fork colocalization protein |
| RA | 4,394,057 | G→A | P4L (CCC→CTC) | queG ← | epoxyqueuosine reductase |
| RA | 4,443,799 | A→G | D473G (GAC→GGC) | tamA → | translocation and assembly module subunit TamA |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,472,426 | (A)8→9 | coding (108/135 nt) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,546,391 | G→A | G432G (GGG→GGA) | fimD → | type I fimbriae usher protein |
| RA | 4,565,618 | C→T | C78Y (TGC→TAC) | yjiM ← | putative dehydratase subunit |
| RA | 4,567,589 | A→G | W311R (TGG→CGG) | mdtM ← | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| RA | 4,568,116 | C→T | G135E (GGG→GAG) | mdtM ← | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| RA | 4,583,950 | T→G | N938H (AAC→CAC) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,589,124 | C→T | intergenic (‑45/+5) | yjiX ← / ← btsT | conserved protein YjiX/pyruvate:H(+) symporter |
| RA | 4,589,872 | C→T | A470T (GCG→ACG) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,606,330 | (G)8→7 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,637,743 | (A)9→8 | coding (1048/1425 nt) | creC → | sensory histidine kinase CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 736858–736904 | 737382–737309 | 406–525 | 18 [17] | [17] 18 | [ybfL] | [ybfL] |
| * | * | ÷ | NC_000913 | 3423764–3424234 | 3424525–3424238 | 5–762 | 18 [17] | [12] 21 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3762347–3764072 | 3765220–3764077 | 6–2874 | 18 [17] | [17] 18 | rhsA | rhs element protein RhsA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 82 (1.110) | 24 (0.370) | 18/244 | 2.1 | 26.3% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 62 (0.950) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 68 (0.950) | 50/268 | 0.2 | 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 = | 138 (1.860) | 115 (1.560) | 59/274 | 0.1 | 62.7% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 75 (1.010) | 44/276 | 0.4 | 93.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.070) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||