![]() |
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 |
JC | 980,293 | 3 bp x 2 | 7.6% | duplication | rpsA → | 30S ribosomal protein S1 |
RA | 1,329,516 | C→T | 100% | H33Y (CAC→TAC) | topA → | DNA topoisomerase I |
JC | 1,733,288 | 8 bp x 2 | 17.7% | duplication | pykF → | pyruvate kinase |
JC | 1,733,579 | 7 bp x 2 | 49.5% | duplication | pykF → | pyruvate kinase |
JC JC | 1,733,647 | IS150 (–) +3 bp | 18.4% | coding (683‑685/1413 nt) | pykF → | pyruvate kinase |
RA | 1,806,030 | C→A | 17.9% | E324* (GAA→TAA) | astD ← | succinylglutamic semialdehyde dehydrogenase |
RA | 2,082,685 | G→A | 16.2% | A494V (GCT→GTT) | yegI ← | hypothetical protein |
RA | 3,293,142 | G→T | 21.1% | L1092F (TTG→TTT) | gltB → | glutamate synthase, large subunit |
RA | 3,750,741 | C→A | 19.1% | L58F (TTG→TTT) | radC ← | DNA repair protein RadC |
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 | 4,100,655 | C→T | 16.6% | M192I (ATG→ATA) | hslU ← | ATP‑dependent protease ATP‑binding subunit |
JC JC | 4,524,522 | IS186 (+) +6 bp | 25.9% | coding (494‑499/549 nt) | fimA → | major type 1 subunit fimbrin (pilin) |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | REL606 | 240075 | 240181 | 107 | 14 [12] | [13] 14 | aspV/yafT | tRNA‑Asp/predicted aminopeptidase |
* | * | ÷ | REL606 | 2041400 | 2041537 | 138 | 14 [13] | [13] 15 | wzx | O antigen translocase (Wzx) |
* | * | ÷ | REL606 | 3119447 | 3119558 | 112 | 14 [13] | [13] 14 | yqiC/ygiL | hypothetical protein/predicted fimbrial‑like adhesin protein |
Unassigned new junction evidence... | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | REL606 | = 310705 | 38 (0.930) | 3 (0.070) | 3/50 | NT | 8.6% | coding (1279/1548 nt) | yahF | predicted acyl‑CoA synthetase with NAD(P)‑binding domain and succinyl‑CoA synthetase domain |
? | REL606 | 580473 = | 26 (0.450) | coding (857/3144 nt) | cusA | copper/silver efflux system, membrane component | |||||
* | ? | REL606 | = 606651 | 20 (0.410) | 6 (0.120) | 5/60 | NT | 20.7% | coding (568/957 nt) | fepB | iron‑enterobactin transporter subunit |
? | REL606 | 3650765 = | 26 (0.450) | intergenic (+46/+141) | cspA/hokA | major cold shock protein/toxic polypeptide, small | |||||
* | ? | REL606 | 640118 = | 35 (0.690) | 6 (0.120) | 3/62 | NT | 13.6% | intergenic (+36/+19) | cspE/ccrB | cold shock protein E/camphor resistance protein CrcB |
? | REL606 | = 2825478 | 41 (0.710) | coding (741/1629 nt) | ECB_02649 | protein similar to L‑ribulokinase AraB | |||||
* | ? | REL606 | = 789257 | 46 (1.000) | 6 (0.130) | 4/56 | NT | 15.2% | intergenic (‑235/+241) | ECB_00726/ECB_00727 | integrase/phage related protein |
? | REL606 | 2994085 = | 21 (0.370) | coding (731/2136 nt) | speC | ornithine decarboxylase, constitutive | |||||
* | ? | REL606 | = 840064 | 30 (0.630) | 4 (0.080) | 3/58 | NT | 12.9% | coding (566/747 nt) | glnH | glutamine ABC transporter periplasmic protein |
? | REL606 | = 1619524 | 24 (0.420) | intergenic (‑133/+84) | rem/hokD | predicted protein/small toxic polypeptide | |||||
* | ? | REL606 | 1109621 = | 28 (0.490) | 7 (0.120) | 5/70 | NT | 18.4% | coding (461/1359 nt) | ycdT | predicted diguanylate cyclase |
? | REL606 | = 3061117 | 34 (0.590) | coding (752/1173 nt) | ECB_02854 | conserved hypothetical protein | |||||
* | ? | REL606 | 1199793 = | 68 (1.290) | 9 (0.170) | 8/64 | NT | 12.6% | coding (22/828 nt) | potB | spermidine/putrescine ABC transporter membrane protein |
? | REL606 | = 1588685 | 57 (0.990) | coding (219/900 nt) | eamA | cysteine and O‑acetyl‑L‑serine efflux system | |||||
* | ? | REL606 | 1241529 = | 31 (0.670) | 7 (0.150) | 4/56 | NT | 21.5% | coding (693/1737 nt) | ycgO | potassium/proton antiporter |
? | REL606 | = 2574504 | 20 (0.350) | intergenic (+346/+472) | sseA/sseB | 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate | |||||
* | ? | REL606 | = 1292269 | 20 (0.470) | 5 (0.120) | 3/52 | NT | 16.4% | intergenic (+110/+34) | galU/hns | glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS |
? | REL606 | = 2173874 | 31 (0.540) | coding (452/1716 nt) | dld | D‑lactate dehydrogenase, FAD‑binding, NADH independent | |||||
* | ? | REL606 | 1340206 = | 27 (0.470) | 6 (0.100) | 3/70 | NT | 15.6% | intergenic (+107/‑86) | yciM/pyrF | hypothetical protein/orotidine 5'‑phosphate decarboxylase |
? | REL606 | 3170213 = | 38 (0.660) | coding (104/1005 nt) | ygjR | predicted NAD(P)‑binding dehydrogenase | |||||
* | ? | REL606 | = 1370723 | 39 (0.880) | 4 (0.090) | 3/54 | NT | 11.9% | coding (447/1293 nt) | ycjN | predicted sugar transporter subunit: periplasmic‑binding component of ABC superfamily |
? | REL606 | = 2574504 | 20 (0.350) | intergenic (+346/+472) | sseA/sseB | 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate | |||||
* | ? | REL606 | = 1400963 | 52 (1.090) | 13 (0.270) | 7/58 | NT | 22.6% | coding (773/1311 nt) | abgA | predicted peptidase, aminobenzoyl‑glutamate utilization protein |
? | REL606 | = 3875872 | 37 (0.640) | intergenic (‑306/+47) | glmU/atpC | bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon | |||||
* | ? | REL606 | = 1619529 | 29 (0.590) | 6 (0.120) | 4/60 | NT | 20.0% | intergenic (‑138/+79) | rem/hokD | predicted protein/small toxic polypeptide |
? | REL606 | 1946064 = | 19 (0.330) | coding (144/390 nt) | cheY | chemotaxis regulator transmitting signal to flagellar motor component | |||||
* | ? | REL606 | = 2081614 | 38 (0.800) | 6 (0.130) | 4/58 | NT | 11.5% | coding (755/1353 nt) | yegD | predicted chaperone |
? | REL606 | 4281474 = | 54 (0.940) | coding (427/2052 nt) | yjcQ | predicted multidrug efflux system component | |||||
* | ? | REL606 | = 2574511 | 22 (0.480) | 4 (0.090) | 4/56 | NT | 10.1% | intergenic (+353/+465) | sseA/sseB | 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate |
? | REL606 | 3715185 = | 49 (0.850) | coding (2195/4851 nt) | ECB_03460 | putative adhesin | |||||
* | ? | REL606 | 3944628 = | 35 (0.730) | 12 (0.250) | 6/58 | NT | 24.5% | intergenic (+17/‑130) | proM/aslB | tRNA‑Pro/predicted regulator of arylsulfatase activity |
? | REL606 | = 4258591 | 39 (0.680) | coding (1180/1350 nt) | yjcD | predicted permease |