mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 120,299 | A→C | 19.0% | V418G (GTG→GGG) | aroP ← | aromatic amino acid transporter |
| RA | 175,537 | T→G | 31.3% | V144G (GTG→GGG) | clcA → | H(+)/Cl(‑) exchange transporter |
| RA | 209,270 | T→G | 9.1% | V217G (GTG→GGG) | accA → | acetyl‑CoA carboxylase, carboxytransferase, alpha subunit |
| RA | 221,963 | A→C | 12.7% | V228G (GTG→GGG) | metN ← | DL‑methionine transporter subunit |
| RA | 230,100 | A→C | 12.4% | V261G (GTG→GGG) | yafC ← | LysR family putative transcriptional regulator |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 278,652 | G→T | 6.1% | L51M (CTG→ATG) | afuC ← | CP4‑6 prophage, putative ferric transporter subunit |
| RA | 320,423 | T→G | 12.8% | V66G (GTG→GGG) | rclR → | reactive chlorine species (RCS)‑specific activator of the rcl genes |
| RA | 422,247 | A→T | 15.3% | Y421F (TAT→TTT) | proY → | proline‑specific permease |
| RA | 469,266 | A→G | 15.0% | G132G (GGA→GGG) | mdlA → | putative multidrug ABC transporter ATPase |
| RA | 525,571 | T→G | 13.5% | W771G (TGG→GGG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| RA | 540,546 | C→T | 12.1% | intergenic (+38/‑19) | allB → / → ybbY | allantoinase/putative uracil/xanthine transporter |
| RA | 602,635 | A→G | 15.6% | E226G (GAG→GGG) | pheP → | phenylalanine transporter |
| RA | 1,061,965 | A→G | 31.9% | E56G (GAG→GGG) | torD → | TorA‑maturation chaperone |
| RA | 1,101,635 | A→T | 22.8% | L17* (TTA→TAA) | csgG ← | curli production assembly/transport outer membrane lipoprotein |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,445,981 | T→G | 29.1% | G34G (GGT→GGG) | ydbL → | DUF1318 family protein |
| JC | 1,707,847 | Δ10 bp | 17.6% | coding (929‑938/2223 nt) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,709,181:1 | +C | 13.4% | coding (40/1059 nt) | rsxD → | SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex |
| RA | 1,878,707 | A→C | 10.1% | T331T (ACA→ACC) | yeaP → | diguanylate cyclase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,085,014 | T→C | 14.5% | E171G (GAG→GGG) | yeeE ← | UPF0394 family inner membrane protein |
| RA | 2,104,337 | T→C | 7.6% | E58G (GAG→GGG) | wbbK ← | lipopolysaccharide biosynthesis protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,169,668 | A→C | 20.0% | intergenic (+57/+25) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon, interrupted by IS3, split galactitol utilization operon repressor, fragment 2, split galactitol utilization operon repressor, interrupted |
| RA | 2,208,990 | A→C | 20.1% | T342T (ACA→ACC) | yehP → | VMA domain putative YehL ATPase stimulator |
| RA | 2,283,057 | C→A | 12.5% | D297Y (GAT→TAT) | yejK ← | spermidine nucleoid‑associated protein |
| JC | 2,391,263:1 | (CAA)2→3 | 12.6% | coding (241/1458 nt) | nuoN ← | NADH:ubiquinone oxidoreductase, membrane subunit N |
| RA | 2,408,081 | A→T | 10.5% | I175F (ATC→TTC) | alaA → | glutamate‑pyruvate aminotransferase, glutamic‑pyruvic transaminase (GPT), alanine transaminase |
| RA | 2,511,394 | T→C | 19.6% | intergenic (+69/+72) | ypeC → / ← mntH | DUF2502 family putative periplasmic protein/manganese/divalent cation transporter |
| RA | 2,596,612 | T→C | 13.1% | I42V (ATA→GTA) | ypfJ ← | putative neutral zinc metallopeptidase |
| RA | 2,819,980:1 | +A | 4.8% | coding (2030/2631 nt) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,849,736 | T→C | 6.9% | R38G (AGA→GGA) | hycB ← | hydrogenase 3, Fe‑S subunit |
| RA | 2,913,629 | T→G | 12.2% | A7A (GCA→GCC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,977,362 | C→T | 11.2% | L256F (CTC→TTC) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| JC | 3,249,103 | Δ12 bp | 2.5% | coding (137‑148/369 nt) | yqjC → | DUF1090 family putative periplasmic protein |
| RA | 3,252,184 | Δ1 bp | 4.2% | intergenic (+176/‑118) | yqjG → / → yhaH | putative S‑transferase/DUF805 family inner membrane protein |
| RA | 3,277,405 | C→T | 12.2% | A24V (GCT→GTT) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,277,446 | G→A | 16.7% | E38K (GAA→AAA) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,277,507 | A→G | 17.1% | E58G (GAG→GGG) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,289,022 | C→A | 15.8% | Q71K (CAA→AAA) | yraJ → | putative outer membrane protein |
| RA | 3,289,076 | C→A | 23.9% | Q89K (CAG→AAG) | yraJ → | putative outer membrane protein |
| RA | 3,327,169 | A→C | 17.4% | V165G (GTG→GGG) | rlmE ← | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 3,335,252 | T→C | 12.8% | E414G (GAG→GGG) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,355,596 | G→C | 6.8% | A292P (GCA→CCA) | gltB → | glutamate synthase, large subunit |
| RA | 3,386,580 | T→C | 6.4% | E536G (GAG→GGG) | aaeB ← | p‑hydroxybenzoic acid efflux system component |
| JC | 3,399,169 | Δ3 bp | 6.3% | coding (806‑808/1104 nt) | mreC ← | cell wall structural complex MreBCD transmembrane component MreC |
| JC | 3,429,830 | (TTC)3→2 | 2.7% | coding (190‑192/258 nt) | yrdB ← | DUF1488 family protein |
| RA | 3,507,166 | T→C | 13.9% | S57G (AGC→GGC) | yhfT ← | inner membrane protein |
| RA | 3,638,227 | A→G | 22.4% | E196G (GAG→GGG) | pitA → | phosphate transporter, low‑affinity, tellurite importer |
| RA | 3,640,983 | C→T | 22.8% | F41F (TTC→TTT) | dtpB → | dipeptide and tripeptide permease B |
| RA | 3,682,103 | T→C | 4.0% | intergenic (‑164/+57) | yhjJ ← / ← dctA | putative periplasmic M16 family chaperone/C4‑dicarboxylic acid, orotate and citrate transporter |
| RA | 3,697,739 | T→G | 18.6% | V428G (GTG→GGG) | bcsE → | cellulose production protein |
| RA | 3,699,265 | T→A | 7.4% | N351K (AAT→AAA) | bcsG → | DUF3260 family cellulose production inner membrane protein |
| RA | 3,791,998 | A→G | 6.9% | S185P (TCA→CCA) | kbl ← | glycine C‑acetyltransferase |
| RA | 3,792,339 | G→A | 9.2% | S71F (TCT→TTT) | kbl ← | glycine C‑acetyltransferase |
| RA | 3,796,792 | A→G | 12.7% | D272G (GAT→GGT) | waaC → | ADP‑heptose:LPS heptosyl transferase I |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,817,495 | T→G | 9.5% | V274G (GTG→GGG) | yicC → | UPF0701 family protein |
| RA | 3,832,076 | G→A | 4.9% | V541M (GTG→ATG) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| JC | 3,984,188 | (AGTA)2→1 | 2.9% | coding (1232‑1235/1236 nt) | aslB → | putative AslA‑specific sulfatase‑maturating enzyme |
| JC | 4,001,644 | Δ5 bp | 94.9% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,027,435 | T→G | 3.9% | intergenic (+208/+173) | fre → / ← fadA | NAD(P)H‑flavin reductase/3‑ketoacyl‑CoA thiolase (thiolase I) |
| RA | 4,056,114 | A→C | 22.8% | G75G (GGT→GGG) | glnL ← | sensory histidine kinase in two‑component regulatory system with GlnG |
| RA | 4,065,570 | T→A | 14.8% | T66S (ACC→TCC) | yihO ← | putative sulphoquinovose importer |
| RA | 4,065,595 | C→A | 18.2% | L57L (CTG→CTT) | yihO ← | putative sulphoquinovose importer |
| RA | 4,065,603 | T→A | 18.6% | I55F (ATC→TTC) | yihO ← | putative sulphoquinovose importer |
| RA | 4,136,803 | A→G | 16.2% | S233G (AGC→GGC) | yijE → | EamA‑like transporter family protein |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,241,837 | G→C | 11.0% | G139G (GGC→GGG) | xylE ← | D‑xylose transporter |
| RA | 4,242,021 | C→A | 13.4% | C78F (TGC→TTC) | xylE ← | D‑xylose transporter |
| RA | 4,268,201 | T→G | 5.7% | R363R (CGT→CGG) | tyrB → | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| RA | 4,277,819 | G→T | 6.0% | G118* (GGA→TGA) | soxR → | redox‑sensitive transcriptional activator of soxS, autorepressor |
| RA | 4,378,891 | C→A | 17.0% | A19S (GCT→TCT) | ampC ← | penicillin‑binding protein, beta‑lactamase, intrinsically weak |
| RA | 4,417,410:1 | +C | 3.9% | coding (458/750 nt) | yjfP → | acyl CoA esterase |
| RA | 4,463,875 | T→G | 15.7% | H279P (CAC→CCC) | treC ← | trehalose‑6‑P hydrolase |
| RA | 4,470,078 | T→G | 17.0% | V818G (GTG→GGG) | mgtA → | magnesium transporter |
| RA | 4,489,904 | A→C | 13.5% | V54G (GTG→GGG) | yjgR ← | DUF853 family protein with NTPase fold |
| RA | 4,530,175 | T→A | 12.4% | I24F (ATC→TTC) | sgcC ← | putative PTS system EIIC permease component |
| RA | 4,588,080 | A→C | 18.7% | W263G (TGG→GGG) | yjiA ← | metal‑binding GTPase |
| RA | 4,594,290 | G→C | 4.8% | A145G (GCG→GGG) | lgoT ← | putative L‑galactonate:H+ symporter |
| RA | 4,606,903 | A→G | 26.7% | S267P (TCC→CCC) | rsmC ← | 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent |
| RA | 4,620,877 | T→C | 3.6% | intergenic (+50/‑7) | deoB → / → deoD | phosphopentomutase/purine nucleoside phosphorylase 1, nicotinamide 1‑beta‑D‑riboside phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 384825 | 385037 | 213 | 17 [11] | [16] 17 | yaiS/tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 1465088 | 1465318 | 231 | 17 [14] | [16] 18 | ynbG | ynbG |
| * | * | ÷ | NC_000913 | 2469259 | 2469572 | 314 | 17 [15] | [16] 17 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 3799034 | 3799361 | 328 | 17 [9] | [15] 17 | [waaU]–[waaZ] | [waaU], [waaZ] |
| * | * | ÷ | NC_000913 | 4233776 | 4235392 | 1617 | 17 [15] | [16] 17 | pgi | glucosephosphate isomerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 82 (1.040) | 53/410 | NT | 97.6% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 2 (0.030) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 458787 = | 5 (0.060) | 90 (1.160) | 57/404 | NT | 94.8% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | = 458799 | 3 (0.040) | 96 (1.250) | 62/402 | NT | 97.0% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | 1207790 = | 24 (0.310) | 84 (1.160) | 59/378 | NT | 84.4% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 9 (0.120) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.290) | 57 (0.790) | 43/378 | NT | 79.1% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 9 (0.120) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 3 (0.040) | 82 (1.040) | 53/410 | NT | 96.5% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 34 (0.440) | 24/402 | NT | 98.6% | 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 | = 1710418 | 40 (0.510) | 3 (0.040) | 3/408 | NT | 7.0% | coding (215/621 nt) | rsxG | SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex |
| ? | NC_000913 | 2101750 = | NA (NA) | intergenic (‑6/+145) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 28 (0.360) | 18/410 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 57 (0.720) | 39/410 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 7 (0.090) | 4/410 | NT | 10.3% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | = 3560228 | 61 (0.780) | pseudogene (224/606 nt) | glpR | pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon | |||||
| * | ? | NC_000913 | = 2290111 | NA (NA) | 6 (0.080) | 5/410 | NT | 8.8% | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| ? | NC_000913 | 3560225 = | 62 (0.790) | pseudogene (227/606 nt) | glpR | pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon | |||||
| * | ? | NC_000913 | 3858192 = | 99 (1.260) | 4 (0.050) | 4/384 | NT | 4.4% | coding (212/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | 3858241 = | 81 (1.100) | coding (163/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein | |||||