mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 69,740 | T→C | 5.6% | H211H (CAT→CAC) | leuO → | DNA‑binding transcriptional activator |
| RA | 130,093 | C→T | 9.5% | D91D (GAC→GAT) | yadE → | predicted polysaccharide deacetylase lipoprotein |
| RA | 130,099 | G→A | 6.9% | L93L (TTG→TTA) | yadE → | predicted polysaccharide deacetylase lipoprotein |
| RA | 130,102 | C→T | 6.6% | G94G (GGC→GGT) | yadE → | predicted polysaccharide deacetylase lipoprotein |
| RA | 139,441 | C→T | 5.6% | S242S (TCG→TCA) | htrE ← | predicted outer membrane usher protein |
| RA | 194,465 | C→T | 5.2% | G124G (GGC→GGT) | nlpE → | lipoprotein involved with copper homeostasis and adhesion |
| RA | 194,492 | T→C | 5.6% | Y133Y (TAT→TAC) | nlpE → | lipoprotein involved with copper homeostasis and adhesion |
| RA | 204,511 | C→T | 100% | intergenic (+111/‑73) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 204,556 | A→G | 100% | intergenic (+156/‑28) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 214,925 | A→C | 82.2% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 214,931 | A→C | 84.7% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 244,761 | C→T | 39.1% | G221R (GGG→AGG) | sbcD ← | exonuclease, dsDNA, ATP‑dependent |
| RA | 253,106 | C→G | 6.7% | P94P (CCG→CCC) | yajB ← | conserved hypothetical protein |
| RA | 253,133 | A→C | 10.0% | L85L (CTT→CTG) | yajB ← | conserved hypothetical protein |
| RA | 253,151 | G→C | 8.5% | V79V (GTC→GTG) | yajB ← | conserved hypothetical protein |
| RA | 316,095 | A→G | 64.2% | N364S (AAC→AGC) | kefA → | fused mechanosensitive channel proteins |
| RA | 327,825 | A→G | 53.9% | R206R (CGT→CGC) | aes ← | acetyl esterase |
| RA | 379,337 | A→G | 63.9% | V24A (GTT→GCT) | fepB ← | iron‑enterobactin transporter subunit |
| RA | 391,026 | T→C | 5.6% | V147V (GTA→GTG) | ybdN ← | conserved hypothetical protein |
| RA | 391,050 | T→A | 5.5% | P139P (CCA→CCT) | ybdN ← | conserved hypothetical protein |
| RA | 391,063 | C→G | 5.9% | C135S (TGC→TCC) | ybdN ← | conserved hypothetical protein |
| RA | 497,847 | A→G | 61.1% | Y222H (TAT→CAT) | galE ← | UDP‑galactose‑4‑epimerase |
| RA | 520,325 | T→C | 50.6% | V115V (GTT→GTC) | uvrB → | excinulease of nucleotide excision repair, DNA damage recognition component |
| RA | 549,018 | A→G | 54.1% | L321L (TTG→CTG) | ybiU ← | hypothetical protein |
| RA | 562,851 | A→G | 44.8% | K116K (AAA→AAG) | ybjK → | predicted DNA‑binding transcriptional regulator |
| RA | 580,895 | C→T | 49.3% | L311L (CTC→CTT) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 626,669 | C→G | 5.5% | D194E (GAC→GAG) | ycaQ → | conserved hypothetical protein |
| RA | 626,673 | G→A | 5.8% | D196N (GAT→AAT) | ycaQ → | conserved hypothetical protein |
| RA | 626,700 | A→G | 6.3% | T205A (ACA→GCA) | ycaQ → | conserved hypothetical protein |
| RA | 627,979 | A→G | 43.0% | K143K (AAA→AAG) | kdsB → | 3‑deoxy‑manno‑octulosonate cytidylyltransferase |
| RA | 667,493 | C→T | 6.3% | R277R (CGC→CGT) | uup → | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 718,738 | A→T | 10.9% | R24R (CGA→CGT) | mviN → | predicted inner membrane protein |
| RA | 726,129 | C→T | 5.5% | T27T (ACC→ACT) | yceD → | conserved hypothetical protein |
| RA | 732,870 | G→A | 6.0% | V106I (GTT→ATT) | pabC → | 4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex |
| RA | 734,169 | C→T | 57.1% | P268L (CCG→CTG) | yceG → | predicted aminodeoxychorismate lyase |
| RA | 735,832 | C→G | 6.2% | G272G (GGC→GGG) | holB → | DNA polymerase III, delta prime subunit |
| RA | 735,840 | C→T | 6.3% | A275V (GCC→GTC) | holB → | DNA polymerase III, delta prime subunit |
| RA | 747,704 | T→C | 5.7% | P128P (CCA→CCG) | ycfQ ← | predicted DNA‑binding transcriptional regulator |
| RA | 757,550 | G→A | 44.4% | A326T (GCA→ACA) | lolE → | outer membrane‑specific lipoprotein transporter subunit |
| RA | 831,492 | T→C | 45.5% | intergenic (+465/‑51) | narK → / → narG | nitrate/nitrite transporter/nitrate reductase 1, alpha subunit |
| RA | 838,839 | T→C | 53.7% | Q10R (CAA→CGA) | tpr ← | predicted protamine‑like protein |
| RA | 887,945 | C→T | 46.2% | E373K (GAG→AAG) | yciW ← | predicted oxidoreductase |
| RA | 894,163 | C→T | 49.0% | A88T (GCG→ACG) | sapB ← | predicted antimicrobial peptide transporter subunit |
| RA | 920,084 | C→T | 9.3% | W172* (TGG→TAG) | mpaA ← | murein peptide amidase A |
| RA | 931,499 | C→T | 5.4% | A239A (GCG→GCA) | yddG ← | predicted methyl viologen efflux pump |
| RA | 931,511 | T→G | 6.4% | V235V (GTA→GTC) | yddG ← | predicted methyl viologen efflux pump |
| RA | 931,514 | A→G | 6.7% | P234P (CCT→CCC) | yddG ← | predicted methyl viologen efflux pump |
| RA | 1,011,820 | C→T | 48.3% | R416R (CGC→CGT) | rstB → | sensory histidine kinase in two‑component regulatory system with RstA |
| RA | 1,011,880 | C→T | 5.3% | intergenic (+6/‑70) | rstB → / → tus | sensory histidine kinase in two‑component regulatory system with RstA/inhibitor of replication at Ter, DNA‑binding protein |
| RA | 1,011,888 | A→G | 6.2% | intergenic (+14/‑62) | rstB → / → tus | sensory histidine kinase in two‑component regulatory system with RstA/inhibitor of replication at Ter, DNA‑binding protein |
| RA | 1,026,281 | A→C | 6.6% | R197R (CGT→CGG) ‡ | malI ← | DNA‑binding transcriptional repressor |
| RA | 1,026,282 | C→A | 6.5% | R197L (CGT→CTT) ‡ | malI ← | DNA‑binding transcriptional repressor |
| RA | 1,036,505 | G→A | 100% | A632A (GCG→GCA) | rsxC → | fused predicted 4Fe‑4S ferredoxin‑type protein |
| RA | 1,118,446 | G→A | 5.9% | P164S (CCA→TCA) | ydiU ← | conserved hypothetical protein |
| RA | 1,118,451 | G→A | 6.0% | A162V (GCG→GTG) | ydiU ← | conserved hypothetical protein |
| RA | 1,136,538 | T→C | 39.7% | K129K (AAA→AAG) | yniB ← | predicted inner membrane protein |
| RA | 1,260,263 | A→G | 6.1% | L221L (TTA→CTA) | torZ ← | trimethylamine N‑oxide reductase system III, catalytic subunit |
| RA | 1,260,264 | G→C | 6.3% | T220T (ACC→ACG) | torZ ← | trimethylamine N‑oxide reductase system III, catalytic subunit |
| RA | 1,266,955 | T→C | 46.2% | E151G (GAA→GGA) | yecA ← | conserved metal‑binding protein |
| RA | 1,289,664 | G→A | 5.5% | L431L (TTG→TTA) | amn → | AMP nucleosidase |
| RA | 1,289,670 | C→T | 5.9% | G433G (GGC→GGT) | amn → | AMP nucleosidase |
| RA | 1,348,785 | G→A | 6.3% | G478G (GGC→GGT) | asmA ← | predicted assembly protein |
| RA | 1,421,965 | T→C | 6.3% | L164L (CTA→CTG) | ccmF ← | heme lyase, CcmF subunit |
| RA | 1,421,968 | C→T | 5.3% | P163P (CCG→CCA) | ccmF ← | heme lyase, CcmF subunit |
| RA | 1,456,456 | A→C | 5.4% | I298M (ATT→ATG) | yfaQ ← | hypothetical protein |
| RA | 1,456,471 | A→G | 6.8% | T293T (ACT→ACC) ‡ | yfaQ ← | hypothetical protein |
| RA | 1,456,473 | T→C | 6.8% | T293A (ACT→GCT) ‡ | yfaQ ← | hypothetical protein |
| RA | 1,470,435 | C→T | 5.3% | Q429Q (CAG→CAA) | yfaL ← | adhesin |
| RA | 1,563,260 | A→G | 5.1% | E1089E (GAA→GAG) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 1,563,284 | C→T | 5.2% | N1097N (AAC→AAT) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 1,568,329 | A→G | 5.5% | L333L (TTG→CTG) | mntH ← | manganese/divalent cation transporter |
| RA | 1,587,720 | A→G | 5.6% | L199L (CTA→CTG) | ptsI → | PEP‑protein phosphotransferase of PTS system |
| RA | 1,590,902 | A→G | 45.9% | V32V (GTA→GTG) | yfeS → | conserved hypothetical protein |
| RA | 1,730,964 | G→A | 6.3% | R91R (CGC→CGT) | yfhB ← | conserved hypothetical protein |
| RA | 1,730,973 | G→A | 5.2% | R88R (CGC→CGT) | yfhB ← | conserved hypothetical protein |
| RA | 1,730,976 | C→T | 5.2% | V87V (GTG→GTA) | yfhB ← | conserved hypothetical protein |
| RA | 1,763,556 | T→C | 38.8% | noncoding (288/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,636 | A→G | 28.6% | noncoding (208/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,804,090 | G→A | 82.1% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 1,831,530 | A→G | 53.6% | S146G (AGC→GGC) | ygbJ → | predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain |
| RA | 1,892,019:1 | +GC | 100% | intergenic (‑437/+54) | gudP ← / ← ygdL | predicted D‑glucarate transporter/conserved hypothetical protein |
| RA | 1,936,262 | A→G | 5.2% | G371G (GGT→GGC) | recJ ← | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| RA | 1,936,265 | G→A | 5.2% | V370V (GTC→GTT) | recJ ← | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| RA | 1,941,030 | T→G | 5.3% | T150T (ACT→ACG) | ygfZ → | predicted folate‑dependent regulatory protein |
| RA | 1,981,950 | G→A | 5.4% | P42L (CCG→CTG) | yggR ← | predicted transporter |
| RA | 1,981,954 | T→C | 5.6% | T41A (ACG→GCG) | yggR ← | predicted transporter |
| RA | 2,028,050 | G→A | 5.2% | I228I (ATC→ATT) | parC ← | DNA topoisomerase IV, subunit A |
| RA | 2,226,993 | G→A | 5.8% | L22L (CTG→CTA) | yhdY → | predicted amino‑acid transporter subunit |
| RA | 2,327,603 | T→C | 51.3% | F225S (TTT→TCT) | cpxA → | sensory histidine kinase in two‑component regulatory system with CpxR |
| RA | 2,359,867 | G→A | 41.5% | noncoding (1228/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,359,876 | C→T | 36.9% | noncoding (1219/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,373,313 | G→T | 11.4% | R105S (CGC→AGC) | ubiD ← | 3‑octaprenyl‑4‑hydroxybenzoate decarboxylase |
| RA | 2,398,935 | C→T | 5.6% | E566K (GAG→AAG) | uvrD ← | DNA‑dependent ATPase I and helicase II |
| RA | 2,482,946 | A→G | 5.0% | intergenic (‑83/+185) | mdtL ← / ← trmE | multidrug efflux system protein/GTPase |
| RA | 2,512,673 | A→T | 54.6% | intergenic (‑144/‑136) | yicE ← / → gltS | predicted transporter/glutamate transporter |
| RA | 2,513,919 | T→C | 5.9% | F371L (TTT→CTT) | gltS → | glutamate transporter |
| RA | 2,513,959 | T→C | 54.5% | I384T (ATC→ACC) | gltS → | glutamate transporter |
| RA | 2,526,477 | T→C | 5.5% | M169V (ATG→GTG) | ttk ← | division inhibitor |
| RA | 2,531,994 | T→C | 50.7% | L314L (TTA→TTG) | kdtA ← | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase |
| RA | 2,554,520 | G→T | 22.3% | L40I (CTC→ATC) | envC ← | protease with a role in cell division |
| RA | 2,573,001 | C→T | 5.7% | intergenic (+1769/‑10) | yibH → / → ysaB | hypothetical protein/hypothetical protein |
| RA | 2,603,330 | C→T | 5.4% | P447P (CCG→CCA) | yhiP ← | predicted transporter |
| RA | 2,603,348 | C→T | 6.9% | P441P (CCG→CCA) | yhiP ← | predicted transporter |
| RA | 2,603,351 | C→T | 7.5% | V440V (GTG→GTA) | yhiP ← | predicted transporter |
| RA | 2,603,354 | C→T | 9.0% | A439A (GCG→GCA) | yhiP ← | predicted transporter |
| RA | 2,699,171 | C→T | 6.3% | T16T (ACC→ACT) | yrfC → | predicted fimbrial assembly protein |
| RA | 2,739,039 | T→C | 51.6% | G95G (GGT→GGC) | rpsJ → | 30S ribosomal subunit protein S10 |
| RA | 2,797,686 | A→G | 5.1% | L357L (TTA→TTG) | dinF → | DNA‑damage‑inducible SOS response protein |
| RA | 2,837,204 | T→C | 26.1% | E39G (GAA→GGA) | yjeK ← | predicted lysine aminomutase |
| RA | 2,858,365 | G→A | 7.1% | T213T (ACG→ACA) | amiB → | N‑acetylmuramoyl‑l‑alanine amidase II |
| RA | 2,910,037 | C→T | 5.6% | R343R (CGC→CGT) | mgtA → | magnesium transporter |
| RA | 2,910,046 | A→C | 5.2% | V346V (GTA→GTC) | mgtA → | magnesium transporter |
| RA | 2,910,050 | C→T | 5.1% | L348L (CTG→TTG) | mgtA → | magnesium transporter |
| RA | 2,960,872 | G→A | 52.2% | intergenic (+322/+98) | yjjV → / ← yjjW | predicted DNase/predicted pyruvate formate lyase activating enzyme |
| RA | 2,963,081 | G→A | 20.4% | A92V (GCG→GTG) | yjjI ← | conserved hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | minE | 899394 | 899470 | 77 | 21 [18] | [18] 19 | pspD | peripheral inner membrane phage‑shock protein |
| * | * | ÷ | minE | 1616710 | 1616745 | 36 | 21 [18] | [13] 19 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | minE | 183922 = | 64 (0.840) | 43 (0.720) +TTATAACATTT |
18/78 | NT | 43.5% | intergenic (+8/‑29) | rnhB/dnaE | ribonuclease HII, degrades RNA of DNA‑RNA hybrids/DNA polymerase III alpha subunit |
| ? | minE | 974451 = | 79 (1.040) | intergenic (+203/+789) | lsrB/ydeH | AI2 transporter/conserved hypothetical protein | |||||
| * | ? | minE | = 215622 | 31 (0.410) | 196 (5.590) +27 bp |
50/46 | NT | 89.2% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | minE | 2705182 = | 72 (0.950) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | minE | 436259 = | 74 (0.970) | 335 (4.780) | 88/92 | NT | 84.4% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | minE | = 2706018 | 56 (0.800) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | minE | = 436833 | 102 (1.340) | 516 (6.780) | 95/100 | NT | 84.0% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | minE | 1803907 = | 94 (1.230) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | minE | 441587 = | 137 (1.800) | 6 (0.090) | 3/88 | NT | 5.3% | coding (2175/2199 nt) | speF | ornithine decarboxylase isozyme, inducible |
| ? | minE | 441625 = | 95 (1.420) | coding (2137/2199 nt) | speF | ornithine decarboxylase isozyme, inducible | |||||
| * | ? | minE | = 779686 | 90 (1.180) | 6 (0.090) | 3/90 | NT | 7.2% | coding (1/402 nt) | ycgK | hypothetical protein |
| ? | minE | = 779714 | 73 (1.070) | intergenic (‑28/‑181) | ycgK/ycgL | hypothetical protein/conserved hypothetical protein | |||||
| * | ? | minE | = 826008 | 54 (0.710) | 28 (0.480) +ACGGCTACATCA |
6/76 | NT | 37.1% | coding (405/1254 nt) | ychP | predicted invasin |
| ? | minE | 1727040 = | 71 (0.930) | coding (1190/3888 nt) | purL | phosphoribosylformyl‑glycineamide synthetase | |||||
| * | ? | minE | = 1156514 | 39 (0.510) | 8 (0.130) +GATTTGCC |
4/84 | NT | 19.2% | coding (912/1479 nt) | astD | succinylglutamic semialdehyde dehydrogenase |
| ? | minE | 2373301 = | 41 (0.540) | coding (325/1494 nt) | ubiD | 3‑octaprenyl‑4‑hydroxybenzoate decarboxylase | |||||
| * | ? | minE | 1240386 = | 48 (0.630) | 4 (0.060) | 3/82 | NT | 7.7% | intergenic (‑156/‑182) | zwf/yebK | glucose‑6‑phosphate dehydrogenase/predicted DNA‑binding transcriptional regulator |
| ? | minE | 1240465 = | 56 (0.900) | intergenic (‑235/‑103) | zwf/yebK | glucose‑6‑phosphate dehydrogenase/predicted DNA‑binding transcriptional regulator | |||||
| * | ? | minE | = 1586789 | 64 (0.840) | 4 (0.060) | 3/92 | NT | 5.3% | intergenic (+351/‑33) | cysK/ptsH | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr) |
| ? | minE | = 1586812 | 84 (1.200) | intergenic (+374/‑10) | cysK/ptsH | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr) | |||||
| * | ? | minE | = 2232355 | NA (NA) | 4 (0.060) | 3/94 | NT | NA | intergenic (‑11/+183) | rrlD/gltV | 23S ribosomal RNA/tRNA‑Glu |
| ? | minE | = 2232377 | NA (NA) | intergenic (‑33/+161) | rrlD/gltV | 23S ribosomal RNA/tRNA‑Glu | |||||
| * | ? | minE | 2639793 = | 106 (1.390) | 5 (0.070) | 3/90 | NT | 5.1% | coding (718/744 nt) | ugpQ | glycerophosphodiester phosphodiesterase, cytosolic |
| ? | minE | 2639818 = | 91 (1.330) | coding (743/744 nt) coding (429/441 nt) |
ugpQ yhhA |
glycerophosphodiester phosphodiesterase, cytosolic conserved hypothetical protein |
|||||
| * | ? | minE | = 2901256 | 100 (1.310) | 5 (0.080) | 5/82 | NT | 5.7% | intergenic (+17/+28) | cybC/nrdG | ECK4231:JW4195:b4236; cytochrome b562, truncated/anaerobic ribonucleotide reductase activating protein |
| ? | minE | = 2901270 | 82 (1.310) | intergenic (+31/+14) | cybC/nrdG | ECK4231:JW4195:b4236; cytochrome b562, truncated/anaerobic ribonucleotide reductase activating protein | |||||