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breseq version 0.24 revision cd15a9d216e1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | ||||||
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evidence | position | mutation | freq | annotation | gene | description |
JC JC | 16,972 | IS150 (–) +3 bp | 86.1% | intergenic (‑14/‑514) | mokC ← / → nhaA | regulatory protein for HokC, overlaps CDS of hokC/pH‑dependent sodium/proton antiporter |
RA | 380,188 | A→C | 92.6% | F239L (TTT→TTG) | araJ ← | predicted transporter |
RA | 475,288 | +G | 100% | coding (18/1677 nt) | ybaL ← | predicted transporter with NAD(P)‑binding Rossmann‑fold domain |
MC JC | 547,700 | Δ8,224 bp | 100% | IS1‑mediated | [nmpC]–[ECB_00513] | [nmpC], ybcR, ybcS, ybcT, ybcU, ECB_00510, nohB, ECB_00512, [ECB_00513] |
RA | 649,391 | T→A | 100% | I471F (ATC→TTC) | mrdA ← | transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2) |
RA | 683,496 | A→C | 100% | V65G (GTT→GGT) | nagC ← | DNA‑binding transcriptional dual regulator, repressor of N‑acetylglucosamine |
RA | 851,606 | G→A | 18.4% | S3F (TCT→TTT) | ybiU ← | hypothetical protein |
RA | 1,248,380 | A→C | 87.0% | D295E (GAT→GAG) | dhaM ← | fused predicted dihydroxyacetone‑specific PTS enzymes: HPr component/EI component |
RA | 1,329,516 | C→T | 100% | H33Y (CAC→TAC) | topA → | DNA topoisomerase I |
RA | 1,370,728 | G→T | 17.0% | W151L (TGG→TTG) | ycjN → | predicted sugar transporter subunit: periplasmic‑binding component of ABC superfamily |
JC JC | 1,733,647 | IS150 (–) +3 bp | 100% | coding (683‑685/1413 nt) | pykF → | pyruvate kinase |
JC JC | 1,821,525 | IS150 (–) +3 bp | 96.3% | coding (573‑575/1041 nt) | ynjI ← | predicted inner membrane protein |
RA | 2,082,685 | G→A | 92.5% | A494V (GCT→GTT) | yegI ← | hypothetical protein |
RA | 3,155,168 | G→A | 93.0% | G296S (GGC→AGC) | ebgR → | DNA‑binding transcriptional repressor |
JC | 3,289,962 | Δ16 bp | 91.9% | coding (96‑111/4554 nt) | gltB → | glutamate synthase, large subunit |
RA | 3,370,027 | T→A | 100% | K117M (AAG→ATG) | rpsM ← | 30S ribosomal protein S13 |
RA | 3,483,047 | C→A | 100% | R455S (CGC→AGC) | malT → | transcriptional regulator MalT |
RA | 3,762,741 | A→T | 100% | K662I (AAA→ATA) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
MC JC | 3,894,997 | Δ6,934 bp | 100% | IS150‑mediated | rbsD–[yieO] | rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO] |
RA | 3,901,931 | G→T | 6.8% | T163T (ACC→ACA) | yieO ← | predicted multidrug or homocysteine efflux system |
RA | 4,100,655 | C→T | 100% | M192I (ATG→ATA) | hslU ← | ATP‑dependent protease ATP‑binding subunit |
RA | 4,126,699 | Δ1 bp | 90.2% | coding (335/879 nt) | pflC → | pyruvate formate lyase II activase |
RA | 4,141,009 | G→A | 23.6% | E28K (GAA→AAA) | yijC → | DNA‑binding transcriptional repressor |
RA | 4,201,911 | C→T | 81.5% | A217T (GCG→ACG) | iclR ← | DNA‑binding transcriptional repressor |
JC JC | 4,524,522 | IS186 (+) +6 bp | 93.5% | coding (494‑499/549 nt) | fimA → | major type 1 subunit fimbrin (pilin) |
RA | 4,561,446 | C→G | 9.6% | L1097L (CTG→CTC) | hsdR ← | endonuclease R |
RA | 4,561,448 | G→T | 7.6% | L1097M (CTG→ATG) | hsdR ← | endonuclease R |
RA | 4,616,396 | G→A | 100% | G290S (GGC→AGC) | nadR → | nicotinamide‑nucleotide adenylyltransferase |
Unassigned missing coverage evidence | ||||||||||
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seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | REL606 | 240050 | 240202 | 153 | 22 [21] | [20] 22 | aspV/yafT | tRNA‑Asp/predicted aminopeptidase |
* | * | ÷ | REL606 | 2031670–2031702 | 2035060–2034324 | 2623–3391 | 25 [21] | [20] 23 | [manB]–insA‑14 | [manB], manC, insB‑14, insA‑14 |
* | * | ÷ | REL606 | 2035094–2035096 | 2054970–2054943 | 19848–19877 | 90 [6] | [21] 23 | [wbbD]–[cpsG] | 19 genes [wbbD], wbbC, wzy, wbbB, wbbA, vioB, vioA, wzx, rmlC, rfbA, rfbD, rfbB, galF, wcaM, wcaL, wcaK, wzxC, wcaJ, [cpsG] |
* | * | ÷ | REL606 | 3022431 | 3023224 | 794 | 22 [20] | [21] 22 | [ECB_02821] | [ECB_02821] |
Unassigned new junction evidence... | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | REL606 | = 16728 | NA (NA) | 37 (0.700) | 27/60 | NT | 49.3% | noncoding (1343/1343 nt) | IS186 | repeat region |
? | REL606 | 2713428 = | 38 (0.610) | noncoding (77/93 nt) | serV | tRNA‑Ser | |||||
* | ? | REL606 | = 23727 | 0 (0.000) | 31 (0.550) | 22/64 | NT | 100% | noncoding (437/768 nt) | IS1 | repeat region |
? | REL606 | = 666130 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
* | ? | REL606 | = 122311 | 53 (0.880) | 5 (0.080) | 3/68 | NT | 11.1% | coding (227/855 nt) | ampE | predicted inner membrane protein |
? | REL606 | 4291982 = | 27 (0.440) | intergenic (‑169/‑190) | rpiR/rpiB | DNA‑binding transcriptional repressor/ribose‑5‑phosphate isomerase B | |||||
* | ? | REL606 | 221948 = | 52 (0.870) | 4 (0.070) | 4/68 | NT | 7.9% | coding (487/708 nt) | yaeB | hypothetical protein |
? | REL606 | 4351442 = | 41 (0.660) | intergenic (+50/‑88) | groEL/yjeI | chaperonin GroEL/hypothetical protein | |||||
* | ? | REL606 | 241691 = | 0 (0.000) | 60 (1.030) | 36/66 | NT | 100% | noncoding (435/768 nt) | IS1 | repeat region |
? | REL606 | 3893554 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
* | ? | REL606 | 308482 = | 54 (0.870) | 7 (0.110) | 3/70 | NT | 14.1% | coding (554/606 nt) | yahD | predicted transcriptional regulator with ankyrin domain |
? | REL606 | 1580990 = | 31 (0.500) | coding (757/1389 nt) | yneI | predicted aldehyde dehydrogenase | |||||
* | ? | REL606 | 370838 = | 32 (0.570) | 4 (0.070) | 3/64 | NT | 10.8% | intergenic (+30/‑89) | phoA/psiF | bacterial alkaline phosphatase/hypothetical protein |
? | REL606 | 3051517 = | 34 (0.550) | coding (835/1224 nt) | glcF | glycolate oxidase iron‑sulfur subunit | |||||
* | ? | REL606 | 417727 = | 39 (0.820) | 6 (0.130) | 5/54 | NT | 15.2% | coding (682/891 nt) | cyoE | protoheme IX farnesyltransferase |
? | REL606 | 1333598 = | 28 (0.450) | pseudogene (67/129 nt) | yciX | predicted protein; b4522(b4574) | |||||
* | ? | REL606 | 546191 = | 54 (0.960) | 3 (0.050) | 3/64 | NT | 5.3% | coding (346/384 nt) | ybcQ | predicted antitermination protein |
? | REL606 | 4521571 = | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
* | ? | REL606 | 556412 = | 42 (0.790) | 7 (0.130) | 5/60 | NT | 15.7% | coding (1697/2346 nt) | ECB_00513 | conserved hypothetical protein |
? | REL606 | 1539626 = | 33 (0.530) | coding (46/2400 nt) | dos | cAMP phosphodiesterase, heme‑regulated | |||||
* | ? | REL606 | 619117 = | NA (NA) | 9 (0.150) | 8/66 | NT | 15.8% | noncoding (768/768 nt) | IS1 | repeat region |
? | REL606 | = 2997448 | 48 (0.780) | coding (116/903 nt) | ECB_02798 | conserved hypothetical protein | |||||
* | ? | REL606 | 640118 = | 43 (0.790) | 9 (0.160) | 6/62 | NT | 23.1% | intergenic (+36/+19) | cspE/ccrB | cold shock protein E/camphor resistance protein CrcB |
? | REL606 | = 1245375 | 17 (0.280) | coding (66/441 nt) | ycgY | hypothetical protein | |||||
* | ? | REL606 | = 701454 | 36 (0.600) | 9 (0.150) | 5/68 | NT | 32.7% | coding (1102/2199 nt) | speF | ornithine decarboxylase isozyme, inducible |
? | REL606 | 2039202 = | 1 (0.020) | coding (493/747 nt) | wbbA | putative glycosyltransferase WbbA | |||||
* | ? | REL606 | = 783510 | 35 (0.710) | 6 (0.120) | 4/56 | NT | 12.8% | coding (995/1434 nt) | ybhI | predicted transporter |
? | REL606 | = 4141016 | 47 (0.760) | coding (89/705 nt) | yijC | DNA‑binding transcriptional repressor | |||||
* | ? | REL606 | = 784490 | 26 (0.460) | 3 (0.050) | 3/64 | NT | 9.0% | coding (359/2262 nt) | ybhJ | predicted hydratase |
? | REL606 | 3912266 = | 35 (0.570) | intergenic (+46/‑94) | ilvL/ilvG | ilvG operon leader peptide/acetolactate synthase II, valine insensitive, large subunit | |||||
* | ? | REL606 | = 840064 | 34 (0.600) | 6 (0.110) | 5/64 | NT | 14.0% | coding (566/747 nt) | glnH | glutamine ABC transporter periplasmic protein |
? | REL606 | 2842326 = | 40 (0.650) | intergenic (+24/+50) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase | |||||
* | ? | REL606 | 885072 = | 27 (0.510) | 9 (0.170) | 5/60 | NT | 25.7% | coding (35/858 nt) | ECB_00824 | protein similar to retron EC67 DNA adenine methylase |
? | REL606 | 3944634 = | 25 (0.400) | intergenic (+23/‑124) | proM/aslB | tRNA‑Pro/predicted regulator of arylsulfatase activity | |||||
* | ? | REL606 | = 1036073 | 32 (0.580) | 13 (0.240) | 8/62 | NT | 29.2% | intergenic (+45/+31) | ycbG/ompA | hypothetical protein/outer membrane protein A (3a;II*;G;d) |
? | REL606 | = 2540943 | 31 (0.500) | coding (38/1290 nt) | uraA | uracil transporter | |||||
* | ? | REL606 | 1097109 = | 34 (0.740) | 5 (0.110) | 4/52 | NT | 12.0% | intergenic (+12/‑522) | putP/ycdN | proline:sodium symporter/putative membrane protein |
? | REL606 | 4079105 = | 39 (0.630) | coding (903/1035 nt) | rhaT | L‑rhamnose:proton symporter | |||||
* | ? | REL606 | 1241877 = | 37 (0.750) | 8 (0.160) | 3/56 | NT | 19.5% | coding (345/1737 nt) | ycgO | potassium/proton antiporter |
? | REL606 | = 4081036 | 29 (0.470) | intergenic (+124/‑136) | sodA/kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxygluconate permease | |||||
* | ? | REL606 | 1286705 = | 46 (0.930) | 8 (0.160) | 6/56 | NT | 20.0% | intergenic (+29/‑154) | narI/ECB_01206 | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein |
? | REL606 | 1802338 = | 18 (0.290) | intergenic (‑136/+67) | ydjR/spy | hypothetical protein/envelope stress induced periplasmic protein | |||||
* | ? | REL606 | 1299694 = | 34 (0.740) | 11 (0.240) | 5/52 | NT | 29.3% | coding (919/1632 nt) | oppA | oligopeptide transporter subunit |
? | REL606 | = 2574502 | 19 (0.310) | intergenic (+344/+474) | sseA/sseB | 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate | |||||
* | ? | REL606 | 1474796 = | 37 (0.750) | 6 (0.120) | 4/56 | NT | 17.1% | coding (1030/1209 nt) | ydcM | predicted transposase |
? | REL606 | = 2574503 | 21 (0.340) | intergenic (+345/+473) | sseA/sseB | 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate | |||||
* | ? | REL606 | 1525665 = | 73 (1.250) | 11 (0.190) | 11/66 | NT | 13.8% | coding (178/654 nt) | fdnI | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible |
? | REL606 | = 1536792 | 65 (1.050) | coding (223/582 nt) | ddpX | D‑ala‑D‑ala dipeptidase, Zn‑dependent | |||||
* | ? | REL606 | 1529587 = | 69 (1.120) | 5 (0.080) | 4/70 | NT | 9.5% | coding (21/1698 nt) | sfcA | malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme) |
? | REL606 | = 3061121 | 26 (0.420) | coding (756/1173 nt) | ECB_02854 | conserved hypothetical protein | |||||
* | ? | REL606 | = 1619529 | 44 (0.830) | 7 (0.130) | 4/60 | NT | 15.6% | intergenic (‑138/+79) | rem/hokD | predicted protein/small toxic polypeptide |
? | REL606 | = 3069838 | 32 (0.520) | coding (621/1500 nt) | pitB | phosphate transporter | |||||
* | ? | REL606 | 1955860 = | 31 (0.610) | 7 (0.140) | 3/58 | NT | 15.2% | coding (50/888 nt) | motA | flagellar motor protein MotA |
? | REL606 | = 4141016 | 47 (0.760) | coding (89/705 nt) | yijC | DNA‑binding transcriptional repressor | |||||
* | ? | REL606 | 1980072 = | 40 (0.780) | 10 (0.200) | 7/58 | NT | 18.5% | intergenic (+48/‑295) | yodA/yodB | conserved metal‑binding protein/predicted cytochrome |
? | REL606 | 4038529 = | 48 (0.780) | intergenic (+41/‑176) | bipA/yihL | GTP‑binding protein/predicted DNA‑binding transcriptional regulator | |||||
* | ? | REL606 | 2039192 = | 1 (0.020) | 11 (0.190) | 8/64 | NT | 53.7% | coding (503/747 nt) | wbbA | putative glycosyltransferase WbbA |
? | REL606 | 2353393 = | 18 (0.290) | coding (1551/1833 nt) | yfbS | predicted transporter | |||||
* | ? | REL606 | = 2771409 | 56 (1.060) | 4 (0.080) | 3/60 | NT | 8.2% | intergenic (‑219/‑33) | cysD/iap | sulfate adenylyltransferase subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion |
? | REL606 | 4412609 = | 34 (0.550) | intergenic (‑376/‑158) | ECB_04076/ytfA | putative oxoacyl reductase/predicted transcriptional regulator | |||||
* | ? | REL606 | 2822187 = | NA (NA) | 32 (0.570) | 26/64 | NT | 54.2% | noncoding (768/768 nt) | IS1 | repeat region |
? | REL606 | = 2997504 | 27 (0.440) | coding (172/903 nt) | ECB_02798 | conserved hypothetical protein | |||||
* | ? | REL606 | = 2874421 | 24 (0.450) | 9 (0.170) | 4/60 | NT | 21.7% | coding (780/936 nt) | lysR | DNA‑binding transcriptional dual regulator |
? | REL606 | 3419921 = | 41 (0.660) | coding (282/573 nt) | ppiA | peptidyl‑prolyl cis‑trans isomerase A (rotamase A) | |||||
* | ? | REL606 | = 2886167 | 47 (0.950) | 6 (0.120) | 4/56 | NT | 13.3% | coding (68/2259 nt) | xdhA | xanthine dehydrogenase, molybdenum binding subunit |
? | REL606 | 3650766 = | 31 (0.500) | intergenic (+47/+140) | cspA/hokA | major cold shock protein/toxic polypeptide, small | |||||
* | ? | REL606 | 3082514 = | 43 (0.810) | 8 (0.150) | 5/60 | NT | 15.1% | coding (446/1041 nt) | yghZ | aldo‑keto reductase |
? | REL606 | = 4141016 | 47 (0.760) | coding (89/705 nt) | yijC | DNA‑binding transcriptional repressor | |||||
* | ? | REL606 | 3198500 = | 48 (0.880) | 10 (0.180) | 5/62 | NT | 23.8% | coding (563/990 nt) | tdcB | threonine dehydratase |
? | REL606 | 3424874 = | 16 (0.260) | intergenic (+92/‑34) | nirD/nirC | nitrite reductase small subunit/nitrite transporter | |||||
* | ? | REL606 | 3367495 = | 31 (0.590) | 4 (0.080) | 4/60 | NT | 10.8% | intergenic (‑81/+26) | yhdN/rplQ | hypothetical protein/50S ribosomal protein L17 |
? | REL606 | 3725714 = | 35 (0.570) | coding (68/432 nt) | yibN | predicted rhodanese‑related sulfurtransferase | |||||
* | ? | REL606 | 3893549 = | NA (NA) | 3 (0.060) | 3/60 | NT | NA | intergenic (+4/‑52) | kup/insJ‑5 | potassium transporter/IS150 hypothetical protein |
? | REL606 | = 3894994 | NA (NA) | noncoding (1441/1443 nt) | IS150 | repeat region | |||||
* | ? | REL606 | 3995530 = | 46 (0.870) | 10 (0.190) | 4/60 | NT | 17.7% | coding (58/768 nt) | ECB_03724 | putative transcriptional regulator |
? | REL606 | = 4141016 | 47 (0.760) | coding (89/705 nt) | yijC | DNA‑binding transcriptional repressor |