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 | 4,139 | G→A | 4.7% | D136N (GAT→AAT) ‡ | thrC → | L‑threonine synthase |
| RA | 4,140 | A→T | 4.7% | D136V (GAT→GTT) ‡ | thrC → | L‑threonine synthase |
| RA | 4,141 | T→C | 4.3% | D136D (GAT→GAC) ‡ | thrC → | L‑threonine synthase |
| RA | 19,193 | A→T | 3.0% | E160V (GAA→GTA) | nhaR → | transcriptional activator of nhaA |
| RA | 67,887:1 | +G | 5.6% | coding (451/1503 nt) | araA ← | L‑arabinose isomerase |
| RA | 67,887:2 | +T | 5.6% | coding (451/1503 nt) | araA ← | L‑arabinose isomerase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 307,364 | C→G | 3.8% | A657P (GCT→CCT) | ecpC ← | ECP production outer membrane protein |
| RA | 307,366 | A→T | 3.2% | I656N (ATT→AAT) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 307,367 | T→A | 4.1% | I656F (ATT→TTT) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 307,368 | G→A | 3.1% | N655N (AAC→AAT) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 307,369 | T→A | 3.6% | N655I (AAC→ATC) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 307,370 | T→A | 3.2% | N655Y (AAC→TAC) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 307,371 | T→A | 3.2% | K654N (AAA→AAT) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 307,372 | T→C | 3.2% | K654R (AAA→AGA) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 307,373 | T→A | 3.2% | K654* (AAA→TAA) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 307,374 | A→T | 3.3% | G653G (GGT→GGA) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 307,375 | C→T | 3.2% | G653D (GGT→GAT) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 307,376 | C→G | 3.2% | G653R (GGT→CGT) ‡ | ecpC ← | ECP production outer membrane protein |
| RA | 433,572 | G→A | 2.9% | E40K (GAA→AAA) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| RA | 592,382 | Δ1 bp | 3.4% | coding (797/2238 nt) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 624,544 | Δ1 bp | 4.4% | intergenic (‑34/‑341) | fepB ← / → entC | ferrienterobactin ABC transporter periplasmic binding protein/isochorismate synthase 1 |
| RA | 708,580 | G→A | 2.9% | A83T (GCT→ACT) | chiP → | chitoporin, uptake of chitosugars |
| RA | 711,595 | A→T | 2.9% | intergenic (‑130/+10) | fldA ← / ← ybfE | flavodoxin 1/LexA‑regulated protein, CopB family |
| RA | 720,761 | G→A | 3.0% | S60N (AGC→AAC) | ybfK → | uncharacterized protein |
| RA | 801,312 | A→G | 2.6% | D185G (GAC→GGC) | ybhH → | putative PrpF family isomerase |
| RA | 884,387 | A→G | 7.8% | I239V (ATC→GTC) | mdfA → | multidrug efflux system protein |
| RA | 1,038,564 | G→T | 2.7% | P275P (CCG→CCT) | cbdA → | cytochrome bd‑II oxidase, subunit I |
| 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 | 1,311,197 | G→T | 17.8% | E37* (GAA→TAA) | tonB → | membrane spanning protein in TonB‑ExbB‑ExbD transport complex |
| RA | 1,395,400 | A→T | 2.9% | F175I (TTC→ATC) | ynaI ← | mechanosensitive channel protein, very small conductance |
| RA | 1,466,552 | C→G | 3.8% | pseudogene (1161/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,562 | G→A | 7.6% | pseudogene (1171/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,570 | C→T | 4.5% | pseudogene (1179/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,579 | G→C | 6.8% | pseudogene (1188/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,582 | T→C | 10.7% | pseudogene (1191/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,585 | T→C | 7.8% | pseudogene (1194/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,588 | C→T | 7.3% | pseudogene (1197/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,708,930 | C→A | 9.2% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,925,846 | Δ1 bp | 2.6% | coding (407/657 nt) | yobB → | C‑N hydrolase family protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,020,430 | Δ1 bp | 2.5% | coding (344/1005 nt) | fliM → | flagellar motor switching and energizing component |
| RA | 2,020,431 | Δ1 bp | 2.5% | coding (345/1005 nt) | fliM → | flagellar motor switching and energizing component |
| RA | 2,020,432 | Δ1 bp | 2.5% | coding (346/1005 nt) | fliM → | flagellar motor switching and energizing component |
| JC | 2,023,805 | (CTTTA)2→1 | 14.5% | intergenic (+127/‑159) | fliR → / → rcsA | flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis |
| RA | 2,064,730 | C→G | 3.7% | E165Q (GAA→CAA) | cobS ← | cobalamin synthase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,139,204 | C→A | 3.2% | R435S (CGC→AGC) | yegH → | inner membrane protein |
| RA | 2,304,796 | T→C | 12.1% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,316,392 | A→G | 38.8% | Y73C (TAC→TGC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,316,679 | A→G | 54.2% | T169A (ACC→GCC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,480,272 | A→G | 2.6% | D358G (GAT→GGT) | dsdA → | D‑serine dehydratase |
| RA | 2,486,316:1 | +A | 2.8% | coding (1945/3594 nt) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,486,316:2 | +C | 2.8% | coding (1945/3594 nt) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,565,350 | T→C | 2.6% | intergenic (+20/+129) | yffS → / ← eutA | CPZ‑55 prophage, uncharacterized protein/reactivating factor for ethanolamine ammonia lyase |
| RA | 2,669,057 | T→G | 2.9% | Y10D (TAC→GAC) | hcaE → | 3‑phenylpropionate dioxygenase, large (alpha) subunit |
| RA | 2,721,182 | C→T | 2.6% | S411L (TCG→TTG) | pka → | protein lysine acetyltransferase |
| JC | 2,765,454 | (TATGGCAC)6→5 | 3.2% | intergenic (‑303/+50) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage, uncharacterized protein |
| RA | 2,791,415 | G→T | 2.7% | E49* (GAA→TAA) | gabD → | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| RA | 2,821,222:1 | +G | 2.6% | coding (788/2631 nt) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,821,222:2 | +C | 2.6% | coding (788/2631 nt) | alaS ← | alanyl‑tRNA synthetase |
| RA | 3,030,062 | T→C | 3.0% | I290V (ATC→GTC) | ygfT ← | putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit |
| RA | 3,171,054 | A→T | 2.7% | K191N (AAA→AAT) | qseC → | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB |
| RA | 3,203,787 | A→T | 2.7% | S115T (TCA→ACA) | bacA ← | undecaprenyl pyrophosphate phosphatase |
| RA | 3,205,924 | T→C | 2.8% | I111V (ATT→GTT) | ttdR ← | transcriptional activator of ttdABT |
| RA | 3,355,596 | G→C | 4.1% | A292P (GCA→CCA) | gltB → | glutamate synthase, large subunit |
| RA | 3,527,589 | C→T | 60.6% | Q375* (CAG→TAG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,614,724 | C→T | 2.6% | D353D (GAC→GAT) | nikA → | nickel/heme ABC transporter periplasmic binding protein |
| RA | 3,703,640 | A→G | 4.4% | F70L (TTT→CTT) | dppD ← | dipeptide/heme ABC transporter ATPas |
| RA | 3,770,761 | T→A | 3.3% | L206F (TTA→TTT) | yibH ← | putative membrane fusion protein (MFP) component of efflux pump |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,872,159 | A→T | 3.3% | V280E (GTG→GAG) | dgoD ← | D‑galactonate dehydratase |
| RA | 3,992,437 | T→G | 38.5% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,094,327 | A→C | 3.0% | intergenic (‑56/+395) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,122,432:1 | +G | 2.7% | coding (907/960 nt) | ftsN ← | essential cell division protein |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,261,044 | T→C | 3.0% | R149R (CGT→CGC) | yjbM → | uncharacterized protein |
| RA | 4,296,189 | A→G | 35.1% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 45.9% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 21.3% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,285 | C→T | 8.9% | intergenic (+492/+152) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,423,641 | G→A | 3.0% | A265A (GCG→GCA) | ulaE → | L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 4,529,366 | A→G | 3.6% | T293T (ACT→ACC) | sgcC ← | putative PTS system EIIC permease component |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533682 | 2536419 | 2738 | 80 [70] | [75] 80 | ptsH–[pdxK] | ptsH, ptsI, crr, [pdxK] |
| * | * | ÷ | NC_000913 | 3423805–3424415 | 3424415 | 1–611 | 76 [75] | [75] 76 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4138 | 139 (0.930) | 7 (0.050) | 7/484 | NT | 4.9% | coding (405/1287 nt) | thrC | L‑threonine synthase |
| ? | NC_000913 | = 4141 | 136 (0.940) | coding (408/1287 nt) | thrC | L‑threonine synthase | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 126 (0.850) | 81/498 | NT | 99.2% | 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 | 307356 = | 124 (0.830) | 7 (0.050) | 6/482 | NT | 5.8% | coding (1977/2526 nt) | ecpC | ECP production outer membrane protein |
| ? | NC_000913 | 307385 = | 109 (0.760) | coding (1948/2526 nt) | ecpC | ECP production outer membrane protein | |||||
| * | ? | NC_000913 | = 1147651 | 144 (0.970) | 4 (0.030) | 4/488 | NT | 2.8% | coding (31/1071 nt) | plsX | putative phosphate acyltransferase |
| ? | NC_000913 | = 1147675 | 135 (0.930) | coding (55/1071 nt) | plsX | putative phosphate acyltransferase | |||||
| * | ? | NC_000913 | 1207790 = | 80 (0.540) | 87 (0.620) | 65/466 | NT | 54.9% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 68 (0.490) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 78 (0.520) | 74 (0.530) | 55/466 | NT | 51.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 68 (0.490) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 8 (0.050) | 170 (1.140) | 102/498 | NT | 95.5% | 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 | = 1735204 | 148 (0.990) | 4 (0.030) | 4/484 | NT | 2.7% | coding (770/816 nt) | mepH | murein DD‑endopeptidase, space‑maker hydrolase |
| ? | NC_000913 | = 1735210 | 144 (1.000) | coding (776/816 nt) | mepH | murein DD‑endopeptidase, space‑maker hydrolase | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 91 (0.610) | 47/498 | 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) | 134 (0.900) | 76/498 | 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 | 2288918 = | NA (NA) | 90 (0.610) | 61/496 | NT | 58.9% | intergenic (‑6/+145) | 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 | 3992703 = | 63 (0.420) | coding (1552/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 88 (0.590) | 64/496 | NT | 57.6% | intergenic (‑31/+2) | 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 | = 3992708 | 65 (0.440) | coding (1557/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 2791412 | 134 (0.900) | 4 (0.030) | 4/484 | NT | 3.0% | coding (142/1449 nt) | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| ? | NC_000913 | = 2791419 | 132 (0.910) | coding (149/1449 nt) | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent | |||||
| * | ? | NC_000913 | = 3217373 | 135 (0.910) | 4 (0.030) | 4/482 | NT | 2.7% | coding (597/624 nt) | yqjI | PadR family putative transcriptional regulator |
| ? | NC_000913 | = 3217417 | 161 (1.120) | intergenic (+17/+137) | yqjI/aer | PadR family putative transcriptional regulator/fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component | |||||
| * | ? | NC_000913 | = 3349890 | 113 (0.760) | 3 (0.020) | 3/466 | NT | 2.7% | coding (568/654 nt) | elbB | isoprenoid biosynthesis protein with amidotransferase‑like domain |
| ? | NC_000913 | = 3349874 | 108 (0.780) | coding (584/654 nt) | elbB | isoprenoid biosynthesis protein with amidotransferase‑like domain | |||||
| * | ? | NC_000913 | 3845530 = | 110 (0.740) | 8 (0.060) | 8/478 | NT | 8.2% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992759 | 73 (0.510) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||