mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 178,678 | G→A | 5.6% | A159V (GCG→GTG) | mtn ← | 5'‑methylthioadenosine/S‑adenosylhomocysteine nucleosidase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,075 | G→A | 5.3% | intergenic (+194/‑384) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 588,640 | T→C | 5.2% | Y772C (TAT→TGT) | nfrA ← | bacteriophage N4 receptor, outer membrane subunit |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| 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 | 1,546,717 | Δ1 bp | 6.2% | coding (453/882 nt) | yddG ← | aromatic amino acid exporter |
| RA | 1,708,814 | A→G | 11.2% | A632A (GCA→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,844 | C→G | 14.2% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,847 | G→A | 15.4% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,762,328 | A→G | 6.0% | F62S (TTC→TCC) | sufC ← | SufBCD Fe‑S cluster assembly scaffold protein, ATP‑binding protein |
| RA | 1,847,340 | T→C | 5.4% | K223K (AAA→AAG) | selD ← | selenophosphate synthase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| JC JC | 2,024,155 | IS5 (+) +4 bp | 100% | coding (188‑191/624 nt) | rcsA → | transcriptional regulator of colanic acid capsular biosynthesis |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,304,798 | T→C | 15.5% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,509,497 | C→G | 100% | intergenic (‑71/‑133) | glk ← / → yfeO | glucokinase/putative ion channel protein |
| RA | 2,639,635 | Δ1 bp | 6.9% | coding (941/1275 nt) | hisS ← | histidyl tRNA synthetase |
| RA | 2,903,485 | T→C | 5.5% | intergenic (+111/+1262) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 3,088,095 | T→A | 100% | intergenic (+235/‑189) | metK → / → galP | S‑adenosylmethionine synthetase/D‑galactose transporter |
| RA | 3,321,019 | C→A | 6.8% | E199* (GAG→TAG) | yhbX ← | putative EptAB family phosphoethanolamine transferase, inner membrane protein |
| JC JC | 3,526,449 | IS5 (+) +4 bp | 100% | intergenic (‑300/‑17) | nudE ← / → yrfF | adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,190 | A→G | 28.0% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 28.3% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 23.4% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 10.4% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,410,508 | G→T | 5.6% | E126* (GAA→TAA) | yjfI → | DUF2170 family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533684 | 2536393 | 2710 | 27 [23] | [22] 24 | ptsH–[pdxK] | ptsH,ptsI,crr,[pdxK] |
| * | * | ÷ | NC_000913 | 3423894–3424405 | 3424405 | 1–512 | 24 [22] | [23] 25 | rrlD | 23S ribosomal RNA of rrnD operon |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 38 (0.510) | 22 (0.310) | 20/480 | NT | 41.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 27 (0.390) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 37 (0.500) | 43 (0.610) | 34/480 | NT | 58.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 27 (0.390) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3051052 = | 43 (0.580) | 3 (0.040) | 3/486 | NT | 6.0% | intergenic (‑385/+63) | gcvT/ubiI | aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent |
| ? | NC_000913 | 3051235 = | 53 (0.750) | coding (1083/1203 nt) | ubiI | 2‑octaprenylphenol hydroxylase, FAD‑dependent | |||||
| * | ? | NC_000913 | 3845531 = | 62 (0.830) | 87 (1.210) | 58/492 | NT | 57.5% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992760 | 69 (0.960) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||