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breseq version 0.24 revision cd15a9d216e1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | ||||||
---|---|---|---|---|---|---|
evidence | position | mutation | freq | annotation | gene | description |
RA | 74,220 | G→T | 14.4% | L22F (TTG→TTT) | yabI → | conserved inner membrane protein |
RA | 166,265 | C→A | 28.4% | A437E (GCA→GAA) | hrpB → | predicted ATP‑dependent helicase |
RA | 380,188 | A→C | 40.7% | 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 | 980,180 | A→G | 60.3% | D365G (GAC→GGC) | rpsA → | 30S ribosomal protein S1 |
RA | 1,329,516 | C→T | 100% | H33Y (CAC→TAC) | topA → | DNA topoisomerase I |
JC JC | 1,733,647 | IS150 (–) +3 bp | 98.2% | coding (683‑685/1413 nt) | pykF → | pyruvate kinase |
JC JC | 1,764,698 | IS1 (–) +9 bp | 52.5% | intergenic (‑318/‑7) | ppsA ← / → ydiA | phosphoenolpyruvate synthase/hypothetical protein |
RA | 1,976,879 | T→G | 40.5% | intergenic (‑57/‑76) | yedW ← / → yedX | predicted DNA‑binding response regulator in two‑component system with YedV/hypothetical protein |
RA | 1,992,583 | Δ1 bp | 9.1% | coding (942/1317 nt) | shiA → | shikimate transporter |
RA | 2,082,685 | G→A | 100% | A494V (GCT→GTT) | yegI ← | hypothetical protein |
RA | 2,329,291 | A→T | 20.6% | A22A (GCA→GCT) | elaD → | predicted enzyme |
RA | 2,336,064 | T→G | 15.4% | I168L (ATC→CTC) | nuoM ← | NADH dehydrogenase subunit M |
RA | 2,342,867 | T→G | 13.4% | Q299P (CAG→CCG) | nuoG ← | NADH dehydrogenase subunit G |
RA | 2,499,315 | G→A | 36.6% | intergenic (‑110/‑179) | maeB ← / → talA | malic enzyme/transaldolase A |
RA | 3,045,069 | G→T | 46.7% | T312N (ACC→AAC) | yghJ ← | predicted inner membrane lipoprotein |
RA | 3,248,957 | A→T | 100% | D764E (GAT→GAA) | infB ← | translation initiation factor IF‑2 |
JC | 3,289,962 | Δ16 bp | 39.4% | coding (96‑111/4554 nt) | gltB → | glutamate synthase, large subunit |
RA | 3,339,158 | A→C | 54.9% | intergenic (+22/‑4) | yhdG → / → fis | tRNA‑dihydrouridine synthase B/DNA‑binding protein Fis |
RA | 3,370,027 | T→A | 59.4% | 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 |
RA | 3,875,625 | +T | 100% | intergenic (‑59/+294) | glmU ← / ← atpC | bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon |
RA | 3,893,550 | +G | 52.5% | intergenic (+5/‑51) | kup → / → insJ‑5 | potassium transporter/IS150 hypothetical protein |
RA | 3,893,550 | +G | 13.6% | intergenic (+5/‑51) | kup → / → insJ‑5 | potassium transporter/IS150 hypothetical protein |
MC JC | 3,894,997 | Δ6,934 bp | 100% | IS150‑mediated | rbsD–[yieO] | rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO] |
RA | 4,100,655 | C→T | 100% | M192I (ATG→ATA) | hslU ← | ATP‑dependent protease ATP‑binding subunit |
RA | 4,126,699 | Δ1 bp | 50.0% | coding (335/879 nt) | pflC → | pyruvate formate lyase II activase |
RA | 4,266,356 | G→C | 33.3% | intergenic (‑52/‑341) | acs ← / → nrfA | acetyl‑coenzyme A synthetase/nitrite reductase, formate‑dependent, cytochrome |
RA | 4,366,935 | G→T | 24.2% | A197A (GCC→GCA) | yjeP ← | predicted mechanosensitive channel |
JC JC | 4,524,522 | IS186 (+) +6 bp | 68.8% | coding (494‑499/549 nt) | fimA → | major type 1 subunit fimbrin (pilin) |
RA | 4,560,632 | T→C | 30.9% | Y131C (TAC→TGC) | hsdM ← | DNA methylase M |
RA | 4,616,396 | G→A | 9.9% | 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 | 240089 | 240201 | 113 | 16 [12] | [15] 16 | aspV/yafT | tRNA‑Asp/predicted aminopeptidase |
* | * | ÷ | REL606 | 558854 | 558932 | 79 | 16 [15] | [14] 16 | ECB_00517/appY | conserved hypothetical protein/DNA‑binding transcriptional activator |
* | * | ÷ | REL606 | 2041399 | 2041556 | 158 | 16 [15] | [15] 20 | wzx | O antigen translocase (Wzx) |
* | * | ÷ | REL606 | 2792257 | 2792361 | 105 | 17 [13] | [15] 16 | ygcE/ECB_02621 | predicted kinase/conserved hypothetical protein |
* | * | ÷ | REL606 | 3022861 | 3023156 | 296 | 17 [14] | [15] 18 | ECB_02821/ECB_02822 | hypothetical protein/bifunctional Ribulose 5‑phosphate reductase/CDP‑ribitol pyrophosphorylase |
* | * | ÷ | REL606 | 3119448 | 3119564 | 117 | 16 [14] | [14] 16 | yqiC/ygiL | hypothetical protein/predicted fimbrial‑like adhesin protein |
* | * | ÷ | REL606 | 3692607 | 3692700 | 94 | 16 [15] | [15] 16 | yiaY/selB | predicted Fe‑containing alcohol dehydrogenase/selenocysteinyl‑tRNA‑specific translation factor |
Unassigned new junction evidence... | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | REL606 | 308482 = | 44 (0.720) | 9 (0.150) | 6/70 | NT | 20.2% | coding (554/606 nt) | yahD | predicted transcriptional regulator with ankyrin domain |
? | REL606 | 1580990 = | 27 (0.440) | coding (757/1389 nt) | yneI | predicted aldehyde dehydrogenase | |||||
* | ? | REL606 | 501044 = | 30 (0.560) | 3 (0.060) | 3/62 | NT | 9.1% | coding (238/261 nt) | ybbD | hypothetical protein |
? | REL606 | 4395045 = | 30 (0.490) | intergenic (‑120/‑62) | yjfO/yjfP | hypothetical protein/predicted hydrolase | |||||
* | ? | REL606 | = 590471 | NA (NA) | 9 (0.160) | 9/64 | NT | 16.7% | noncoding (1977/1977 nt) | IS150 | repeat region |
? | REL606 | = 1821527 | 45 (0.740) | coding (573/1041 nt) | ynjI | predicted inner membrane protein | |||||
* | ? | REL606 | = 592057 | NA (NA) | 5 (0.100) | 5/60 | NT | 10.9% | noncoding (1343/1343 nt) | IS186 | repeat region |
? | REL606 | 1391825 = | 41 (0.680) | coding (230/1614 nt) | mppA | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit | |||||
* | ? | REL606 | = 606651 | 22 (0.420) | 6 (0.120) | 3/60 | NT | 18.8% | coding (568/957 nt) | fepB | iron‑enterobactin transporter subunit |
? | REL606 | 3650765 = | 30 (0.490) | intergenic (+46/+141) | cspA/hokA | major cold shock protein/toxic polypeptide, small | |||||
* | ? | REL606 | 640118 = | 36 (0.670) | 11 (0.200) | 6/62 | NT | 20.9% | intergenic (+36/+19) | cspE/ccrB | cold shock protein E/camphor resistance protein CrcB |
? | REL606 | 3995534 = | 47 (0.770) | coding (54/768 nt) | ECB_03724 | putative transcriptional regulator | |||||
* | ? | REL606 | 1286705 = | 38 (0.780) | 7 (0.140) | 4/56 | NT | 17.5% | intergenic (+29/‑154) | narI/ECB_01206 | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein |
? | REL606 | = 2173876 | 28 (0.460) | coding (454/1716 nt) | dld | D‑lactate dehydrogenase, FAD‑binding, NADH independent | |||||
* | ? | REL606 | 1286707 = | 35 (0.670) | 6 (0.120) | 3/60 | NT | 16.0% | intergenic (+31/‑152) | narI/ECB_01206 | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein |
? | REL606 | = 3571661 | 28 (0.460) | coding (110/1470 nt) | yhiP | predicted transporter | |||||
* | ? | REL606 | = 1460974 | NA (NA) | 12 (0.200) | 7/70 | NT | NA | intergenic (+62/‑37) | insB‑12/cybB | IS1 protein InsB/cytochrome b561 |
? | REL606 | 2332094 = | NA (NA) | intergenic (+34/‑53) | yfbM/ECB_02199 | hypothetical protein/PROBABLE ISRSO11‑TRANSPOSASE ORFA PROTEIN | |||||
* | ? | REL606 | 1462251 = | 34 (0.730) | 6 (0.130) | 6/54 | NT | 11.4% | intergenic (‑13/‑328) | mokB/trg | regulatory peptide/methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor |
? | REL606 | = 3413922 | 59 (0.970) | intergenic (‑199/‑103) | yhfA/crp | hypothetical protein/DNA‑binding transcriptional dual regulator | |||||
* | ? | REL606 | 1474796 = | 36 (0.740) | 9 (0.190) | 6/56 | NT | 25.7% | coding (1030/1209 nt) | ydcM | predicted transposase |
? | REL606 | = 2574503 | 16 (0.260) | intergenic (+345/+473) | sseA/sseB | 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate | |||||
* | ? | REL606 | 1732688 = | 44 (0.940) | 5 (0.110) | 3/54 | NT | 14.5% | intergenic (‑280/‑277) | ydhZ/pykF | hypothetical protein/pyruvate kinase |
? | REL606 | 2148171 = | 15 (0.250) | coding (501/3795 nt) | molR | molybdate metabolism regulator | |||||
* | ? | REL606 | = 1922672 | 45 (0.860) | 4 (0.080) | 4/60 | NT | 10.7% | coding (683/786 nt) | znuB | high‑affinity zinc transporter membrane component |
? | REL606 | = 1983317 | 22 (0.360) | coding (456/7152 nt) | yeeJ | adhesin | |||||
* | ? | REL606 | 1946057 = | 48 (0.990) | 8 (0.160) | 3/56 | NT | 20.0% | coding (151/390 nt) | cheY | chemotaxis regulator transmitting signal to flagellar motor component |
? | REL606 | = 2574503 | 16 (0.260) | intergenic (+345/+473) | sseA/sseB | 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate | |||||
* | ? | REL606 | = 2305718 | 51 (0.840) | 9 (0.150) | 4/70 | NT | 19.6% | coding (948/1290 nt) | yfaV | predicted transporter |
? | REL606 | 3065531 = | 23 (0.380) | coding (965/1350 nt) | yghQ | predicted inner membrane protein | |||||
* | ? | REL606 | = 2309352 | 40 (0.770) | 5 (0.100) | 3/60 | NT | 13.7% | coding (795/1203 nt) | yfaY | competence damage‑inducible protein A |
? | REL606 | 3944634 = | 23 (0.380) | intergenic (+23/‑124) | proM/aslB | tRNA‑Pro/predicted regulator of arylsulfatase activity | |||||
* | ? | REL606 | = 2333536 | NA (NA) | 45 (0.740) | 30/70 | NT | 54.9% | noncoding (1441/1441 nt) | ISRSO11 | repeat region |
? | REL606 | 4415710 = | 37 (0.610) | coding (848/1413 nt) | cycA | D‑alanine/D‑serine/glycine transporter | |||||
* | ? | REL606 | = 2408209 | NA (NA) | 5 (0.090) | 5/64 | NT | 6.9% | noncoding (1/768 nt) | IS1 | repeat region |
? | REL606 | = 4621899 | 68 (1.120) | coding (7/522 nt) | yjjX | NTPase | |||||
* | ? | REL606 | = 2574511 | 22 (0.470) | 8 (0.170) | 5/54 | NT | 27.1% | intergenic (+353/+465) | sseA/sseB | 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate |
? | REL606 | 4356096 = | 21 (0.350) | coding (338/537 nt) | blc | outer membrane lipoprotein (lipocalin) | |||||
* | ? | REL606 | 3434228 = | 46 (1.020) | 6 (0.130) | 4/52 | NT | 13.8% | noncoding (2/768 nt) | IS1 | repeat region |
? | REL606 | = 4568881 | 29 (0.480) | coding (374/2151 nt) | yjiY | predicted inner membrane protein | |||||
* | ? | REL606 | = 3530577 | 43 (0.800) | 11 (0.200) | 5/62 | NT | 22.0% | intergenic (‑234/+37) | livJ/rpoH | leucine/isoleucine/valine transporter subunit/RNA polymerase sigma factor |
? | REL606 | 4043869 = | 35 (0.580) | coding (155/1404 nt) | yihO | predited transporter | |||||
* | ? | REL606 | = 4202349 | 37 (0.630) | 38 (0.640) | 29/68 | NT | 51.7% | coding (211/825 nt) | iclR | DNA‑binding transcriptional repressor |
? | REL606 | 4202661 = | 34 (0.560) | intergenic (‑102/‑98) | iclR/metH | DNA‑binding transcriptional repressor/B12‑dependent methionine synthase |