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 | 100,875 | Δ1 bp | 4.0% | coding (111/1476 nt) | murC → | UDP‑N‑acetylmuramate:L‑alanine ligase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 288,136:1 | +A | 5.3% | coding (1348/1611 nt) | yagH → | CP4‑6 prophage, putative xylosidase/arabinosidase |
| RA | 288,136:2 | +G | 5.3% | coding (1348/1611 nt) | yagH → | CP4‑6 prophage, putative xylosidase/arabinosidase |
| RA | 288,136:3 | +C | 5.3% | coding (1348/1611 nt) | yagH → | CP4‑6 prophage, putative xylosidase/arabinosidase |
| RA | 396,190 | T→C | 3.5% | D33G (GAT→GGT) | ampH ← | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase, penicillin‑binding protein, weak beta‑lactamase |
| RA | 433,649 | T→G | 19.9% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| RA | 468,963 | G→A | 4.2% | L31L (CTG→CTA) | mdlA → | putative multidrug ABC transporter ATPase |
| RA | 530,732 | A→C | 19.9% | G165G (GGT→GGG) | mnmH ← | tRNA 2‑selenouridine synthase, selenophosphate‑dependent |
| RA | 540,558 | T→G | 29.2% | intergenic (+50/‑7) | allB → / → ybbY | allantoinase/putative uracil/xanthine transporter |
| RA | 649,766 | T→G | 12.3% | N242T (AAC→ACC) | citE ← | citrate lyase, citryl‑ACP lyase (beta) subunit |
| RA | 712,217 | Δ1 bp | 3.4% | coding (586/765 nt) | ybfF ← | acyl‑CoA esterase |
| RA | 817,818 | A→C | 12.1% | T259P (ACT→CCT) | moaA → | molybdopterin biosynthesis protein A |
| RA | 850,995 | T→G | 3.3% | intergenic (+30/+19) | ompX → / ← opgE | outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 850,996 | C→A | 3.1% | intergenic (+31/+18) | ompX → / ← opgE | outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 850,998 | G→A | 3.3% | intergenic (+33/+16) | ompX → / ← opgE | outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 1,143,829 | A→C | 12.3% | L180R (CTG→CGG) | rne ← | endoribonuclease, RNA‑binding protein,RNA degradosome binding protein |
| RA | 1,196,305 | C→T | 88.9% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,229,521 | G→A | 4.6% | H292Y (CAC→TAC) | hlyE ← | hemolysin E |
| RA | 1,261,470 | Δ1 bp | 2.7% | coding (406/948 nt) | prs ← | phosphoribosylpyrophosphate synthase |
| RA | 1,268,879 | G→T | 15.0% | E239* (GAA→TAA) | kdsA → | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,466,201 | T→C | 6.5% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,210 | G→A | 4.6% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,856 | A→G | 6.1% | pseudogene (1465/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,676,805 | T→G | 16.2% | T367P (ACC→CCC) | pntA ← | pyridine nucleotide transhydrogenase, alpha subunit |
| RA | 1,708,814 | A→G | 6.8% | A632A (GCA→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,890,491 | A→C | 19.4% | G14G (GGT→GGG) | yeaY ← | Slp family lipoprotein, RpoE‑regulated |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,151,689 | G→T | 32.8% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| RA | 2,213,305 | C→A | 3.9% | S446S (TCG→TCT) ‡ | yehU ← | inner membrane putative sensory kinase in two‑component system with YehT |
| RA | 2,213,306 | G→T | 4.2% | S446* (TCG→TAG) ‡ | yehU ← | inner membrane putative sensory kinase in two‑component system with YehT |
| RA | 2,213,308 | C→G | 3.7% | Q445H (CAG→CAC) | yehU ← | inner membrane putative sensory kinase in two‑component system with YehT |
| RA | 2,312,115 | A→C | 18.0% | G211G (GGT→GGG) | ompC ← | outer membrane porin protein C |
| RA | 2,542,927 | G→C | 12.6% | G200G (GGC→GGG) | cysP ← | thiosulfate‑binding protein |
| RA | 2,826,262 | A→G | 12.4% | S145G (AGT→GGT) | srlA → | glucitol/sorbitol‑specific enzyme IIC component of PTS |
| RA | 2,828,504 | T→G | 18.1% | V257G (GTG→GGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 3,206,436 | G→A | 18.6% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,467 | A→G | 16.5% | S3G (AGC→GGC) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,481 | G→A | 29.6% | K7K (AAG→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,482 | C→A | 18.4% | Q8K (CAA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,504 | C→A | 15.0% | T15K (ACA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,285,875 | C→G | 16.4% | P134A (CCG→GCG) | agaD → | N‑acetylgalactosamine‑specific enzyme IID component of PTS |
| JC | 3,491,753 | Δ3 bp | 2.9% | coding (541‑543/573 nt) | ppiA ← | peptidyl‑prolyl cis‑trans isomerase A (rotamase A) |
| RA | 3,520,794 | G→T | 11.5% | T75K (ACA→AAA) | hofP ← | DNA catabolic protein |
| RA | 3,669,058 | C→T | 3.9% | V44I (GTC→ATC) | yhjA ← | putative cytochrome C peroxidase |
| RA | 3,723,394:1 | +G | 3.6% | coding (1003/2070 nt) | glyS ← | glycine tRNA synthetase, beta subunit |
| RA | 3,723,394:2 | +A | 3.6% | coding (1003/2070 nt) | glyS ← | glycine tRNA synthetase, beta subunit |
| RA | 3,723,394:3 | +A | 3.6% | coding (1003/2070 nt) | glyS ← | glycine tRNA synthetase, beta subunit |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,862,660 | T→G | 41.3% | pseudogene (943/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component |
| RA | 3,895,555 | T→C | 17.2% | M352V (ATG→GTG) | adeP ← | adenine permease, high affinity, adenine:H+ symporter |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,059,309 | Δ1 bp | 3.8% | coding (904/1824 nt) | typA → | GTP‑binding protein |
| RA | 4,065,595 | C→A | 16.6% | L57L (CTG→CTT) | yihO ← | putative sulphoquinovose importer |
| RA | 4,086,038 | A→G | 3.4% | E8E (GAA→GAG) | fdhD → | formate dehydrogenase formation protein |
| RA | 4,094,414 | T→G | 6.5% | intergenic (‑143/+308) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,151,328 | T→G | 16.1% | A590A (GCA→GCC) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,151,331 | G→C | 15.7% | G589G (GGC→GGG) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,205,620 | G→T | 25.7% | S104* (TCA→TAA) | purD ← | phosphoribosylglycinamide synthetase phosphoribosylamine‑glycine ligase |
| RA | 4,209,826 | T→G | 14.8% | noncoding (54/76 nt) | gltV → | tRNA‑Glu |
| RA | 4,325,949 | A→G | 6.1% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,336,882 | T→A | 13.3% | I51F (ATC→TTC) | adiC ← | arginine:agmatine antiporter |
| RA | 4,579,663 | A→C | 11.2% | V60G (GTC→GGC) | symE ← | toxic peptide regulated by antisense sRNA symR |
| RA | 4,606,903 | A→G | 15.6% | S267P (TCC→CCC) | rsmC ← | 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 4233736 | 4235453 | 1718 | 38 [36] | [34] 38 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 106 (1.060) | 69/430 | NT | 99.1% | 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 | 1 (0.010) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 285874 = | 77 (0.770) | 3 (0.030) | 3/414 | NT | 4.1% | coding (480/1383 nt) | yagG | CP4‑6 prophage, putative sugar transporter |
| ? | NC_000913 | 285896 = | 68 (0.710) | coding (502/1383 nt) | yagG | CP4‑6 prophage, putative sugar transporter | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 5 (0.050) | 3/430 | NT | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | NC_000913 | = 375325 | NA (NA) | noncoding (396/436 nt) | REP31 (repetitive extragenic palindromic) element, contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element, contains 9 REP sequences | |||||
| * | ? | NC_000913 | 458787 = | 18 (0.180) | 84 (0.850) | 54/424 | NT | 82.6% | 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 | 14 (0.140) | 102 (1.040) | 65/422 | NT | 88.1% | 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 | = 850992 | 110 (1.100) | 4 (0.040) | 4/408 | NT | 3.5% | intergenic (+27/+22) | ompX/opgE | outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase |
| ? | NC_000913 | = 850998 | 113 (1.190) | intergenic (+33/+16) | ompX/opgE | outer membrane protein X/OPG biosynthetic transmembrane phosphoethanolamine transferase | |||||
| * | ? | NC_000913 | 1207790 = | 33 (0.330) | 66 (0.710) | 47/398 | NT | 68.9% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 29 (0.310) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 34 (0.340) | 77 (0.830) | 46/398 | NT | 71.8% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 29 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 2 (0.020) | 106 (1.060) | 65/430 | NT | 98.1% | 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 | = 1321578 | 87 (0.870) | 4 (0.040) | 4/416 | NT | 4.5% | coding (1369/1563 nt) | trpE | component I of anthranilate synthase |
| ? | NC_000913 | = 1321588 | 86 (0.890) | coding (1359/1563 nt) | trpE | component I of anthranilate synthase | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 27 (0.280) | 23/414 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 40 (0.400) | 23/430 | 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) | 97 (0.970) | 63/430 | 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 | 2449189 = | 59 (0.590) | 3 (0.030) | 3/412 | NT | 5.4% | intergenic (+34/+37) | smrB/yfcO | putative DNA endonuclease/DUF2544 family putative outer membrane protein |
| ? | NC_000913 | 2449211 = | 49 (0.510) | intergenic (+56/+15) | smrB/yfcO | putative DNA endonuclease/DUF2544 family putative outer membrane protein | |||||
| * | ? | NC_000913 | 2514275 = | NA (NA) | 3 (0.030) | 3/424 | NT | 3.9% | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase |
| ? | NC_000913 | = 2536318 | 74 (0.740) | coding (487/510 nt) | crr | glucose‑specific enzyme IIA component of PTS | |||||
| * | ? | NC_000913 | = 2515612 | NA (NA) | 8 (0.080) | 7/426 | NT | 9.8% | intergenic (+171/+29) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase |
| ? | NC_000913 | 2536308 = | 74 (0.740) | coding (477/510 nt) | crr | glucose‑specific enzyme IIA component of PTS | |||||
| * | ? | NC_000913 | = 3620867 | NA (NA) | 3 (0.030) | 3/408 | NT | 3.8% | coding (1677/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3621007 | 80 (0.800) | coding (1817/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3699934 = | 127 (1.270) | 3 (0.030) | 3/418 | NT | 2.5% | intergenic (+42/+45) | bcsG/ldrD | DUF3260 family cellulose production inner membrane protein/toxic polypeptide, small |
| ? | NC_000913 | 3699970 = | 107 (1.100) | intergenic (+78/+9) | bcsG/ldrD | DUF3260 family cellulose production inner membrane protein/toxic polypeptide, small | |||||
| * | ? | NC_000913 | 3984219 = | NA (NA) | 3 (0.030) | 3/416 | NT | NA | noncoding (1/104 nt) | RIP287 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site | RIP287 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3984249 = | NA (NA) | noncoding (31/104 nt) | RIP287 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site | RIP287 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 4160851 = | 73 (0.730) | 15 (0.150) | 13/428 | NT | 17.1% | intergenic (‑62/‑272) | sthA/fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| ? | NC_000913 | = 4499511 | NA (NA) | intergenic (+10/+83) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||
| * | ? | NC_000913 | = 4160857 | 78 (0.780) | 3 (0.030) | 3/428 | NT | 3.7% | intergenic (‑68/‑266) | sthA/fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| ? | NC_000913 | 4498183 = | NA (NA) | intergenic (+242/‑90) | intB/insC1 | pseudogene, integrase homology,IS, phage, Tn, Phage‑related functions and prophages, KpLE2 phage‑like element, P4‑like integrase/IS2 repressor TnpA | |||||
| * | ? | NC_000913 | 4542683 = | 28 (0.280) | 3 (0.030) | 3/412 | NT | 5.3% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542997 = | 81 (0.850) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||