mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 17,973:1 | +T | 2.9% | coding (485/1167 nt) | nhaA → | sodium‑proton antiporter |
| RA | 137,235 | T→C | 2.8% | T51T (ACT→ACC) | cueO → | multicopper oxidase (laccase) |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 308,437 | A→G | 7.3% | L299P (CTC→CCC) | ecpC ← | ECP production outer membrane protein |
| RA | 314,213 | Δ1 bp | 4.3% | intergenic (‑408/‑144) | ykgP ← / → eaeH | pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology,factor, Not classified |
| RA | 375,277 | G→A | 3.6% | intergenic (+396/‑182) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 634,091 | T→A | 3.4% | L169H (CTC→CAC) | ybdL → | methionine aminotransferase, PLP‑dependent |
| RA | 731,289 | Δ1 bp | 2.8% | coding (1707/4194 nt) | rhsC → | Rhs protein with putative toxin domain, putative neighboring cell growth inhibitor |
| JC | 822,300 | (AGC)2→1 | 3.1% | coding (197‑199/957 nt) | ybhN ← | UPF0104 family inner membrane protein |
| RA | 911,945 | Δ1 bp | 3.2% | coding (206/969 nt) | hcr ← | HCP oxidoreductase, NADH‑dependent |
| RA | 911,946 | Δ1 bp | 3.2% | coding (205/969 nt) | hcr ← | HCP oxidoreductase, NADH‑dependent |
| RA | 922,735 | C→G | 5.7% | intergenic (‑145/‑178) | cspD ← / → clpS | inhibitor of DNA replication, cold shock protein homolog/regulatory protein for ClpA substrate specificity |
| RA | 1,099,867 | G→A | 2.7% | P76P (CCG→CCA) | ycdY → | redox enzyme maturation protein (REMP) chaperone for YcdX |
| RA | 1,207,333 | Δ1 bp | 2.9% | coding (421/585 nt) | ymfQ → | prohage e14 tail protein homolog |
| RA | 1,567,470 | A→G | 4.8% | intergenic (‑330/+34) | dosC ← / ← yddW | diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog |
| RA | 1,807,196 | T→A | 3.4% | V276D (GTT→GAT) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,968,517:1 | +G | 4.5% | coding (848/861 nt) | cheR ← | chemotaxis regulator, protein‑glutamate methyltransferase |
| RA | 1,968,517:2 | +C | 4.5% | coding (848/861 nt) | cheR ← | chemotaxis regulator, protein‑glutamate methyltransferase |
| RA | 2,066,465 | T→C | 47.1% | K286R (AAG→AGG) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 2,073,151 | Δ1 bp | 3.5% | coding (1613/3120 nt) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,073,152 | Δ1 bp | 3.5% | coding (1614/3120 nt) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,133,285 | A→T | 3.1% | I38N (ATC→AAC) | wcaA ← | putative glycosyl transferase |
| JC | 2,347,199 | Δ87 bp | 2.6% | intergenic (+51/‑97) | nrdA → / → nrdB | ribonucleoside‑diphosphate reductase 1, alpha subunit/ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein |
| RA | 2,350,303 | Δ1 bp | 2.7% | coding (707/1077 nt) | glpQ ← | periplasmic glycerophosphodiester phosphodiesterase |
| RA | 2,440,333 | C→T | 2.8% | intergenic (‑215/+50) | yfcJ ← / ← fabB | putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,511,663 | T→C | 7.4% | I348V (ATT→GTT) | mntH ← | manganese/divalent cation transporter |
| RA | 2,608,975 | Δ1 bp | 2.8% | coding (491/1668 nt) | hyfG → | hydrogenase 4, subunit |
| RA | 2,615,982 | A→G | 3.4% | intergenic (‑103/‑110) | yfgO ← / → bepA | putative UPF0118 family inner membrane permease/OM protein maintenance and assembly metalloprotease and chaperone, periplasmic |
| RA | 3,616,345 | C→A | 3.9% | G55G (GGC→GGA) | nikC → | nickel ABC transporter permease |
| RA | 3,677,391 | G→A | 2.7% | S320L (TCG→TTG) | yhjG ← | putative inner membrane‑anchored periplasmic AsmA family protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,067,678 | A→G | 2.6% | M533T (ATG→ACG) | yihQ ← | putative sulpholipid alpha‑glucosidase, alpha‑glucosyl fluoride glucosidase |
| RA | 4,106,569 | Δ1 bp | 2.9% | coding (102/903 nt) | fieF → | ferrous iron and zinc transporter |
| RA | 4,122,730 | A→G | 5.2% | S203S (TCT→TCC) | ftsN ← | essential cell division protein |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,219,160 | T→C | 8.7% | L189P (CTC→CCC) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,296,189 | A→G | 25.9% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 23.0% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,543,247 | C→T | 2.6% | C44C (TGC→TGT) | fimA → | major type 1 subunit fimbrin (pilin) |
| RA | 4,614,504 | T→C | 4.7% | intergenic (+243/+177) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 4233780 | 4235410 | 1631 | 32 [25] | [29] 32 | [pgi] | [pgi] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 126 (0.840) | 76/480 | NT | 100% | 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 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 25 (0.170) | 81 (0.580) | 56/448 | NT | 77.4% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 24 (0.170) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 24 (0.160) | 125 (0.900) | 78/448 | NT | 84.3% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 24 (0.170) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 128 (0.860) | 79/480 | NT | 100% | 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 | 0 (0.000) | 52 (0.350) | 42/472 | 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 | 1571552 = | 49 (0.330) | 3 (0.020) | 3/474 | NT | 4.9% | coding (494/1401 nt) | gadB | glutamate decarboxylase B, PLP‑dependent |
| ? | NC_000913 | = 3667082 | 67 (0.450) | coding (498/1401 nt) | gadA | glutamate decarboxylase A, PLP‑dependent | |||||
| * | ? | NC_000913 | = 1907503 | 119 (0.800) | 3 (0.020) | 3/470 | NT | 2.6% | coding (89/144 nt) | yobF | DUF2527 family heat‑induced protein |
| ? | NC_000913 | = 1908412 | 112 (0.770) | coding (137/288 nt) | yebO | putative inner membrane protein | |||||
| * | ? | NC_000913 | 1951305 = | 89 (0.600) | 3 (0.020) | 3/462 | NT | 3.0% | coding (474/567 nt) | yecD | isochorismatase family protein |
| ? | NC_000913 | 1951547 = | 107 (0.750) | coding (153/819 nt) | yecE | UPF0759 family protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 47 (0.330) | 32/464 | 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) | 71 (0.480) | 54/480 | 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) | 109 (0.730) | 66/480 | 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 | 4295831 = | NA (NA) | 11 (0.090) | 4/402 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||