mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 102,146 | T→A | 4.2% | L461H (CTC→CAC) | murC → | UDP‑N‑acetylmuramate:L‑alanine ligase |
| RA | 178,678 | G→A | 5.5% | A159V (GCG→GTG) | mtn ← | 5'‑methylthioadenosine/S‑adenosylhomocysteine nucleosidase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,075 | G→A | 5.2% | 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 |
| RA | 825,815 | C→T | 4.6% | L98L (CTG→CTA) | ybhR ← | putative ABC transporter permease |
| RA | 1,270,301 | T→C | 4.4% | A15A (GCA→GCG) | ldrC ← | toxic polypeptide, small |
| RA | 1,270,320 | A→G | 4.3% | I9T (ATT→ACT) | ldrC ← | toxic polypeptide, small |
| 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 | 1,466,276 | T→C | 10.8% | pseudogene (885/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,546,717 | Δ1 bp | 6.2% | coding (453/882 nt) | yddG ← | aromatic amino acid exporter |
| RA | 1,708,844 | C→G | 14.5% | 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 | 18.8% | 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 | 5.9% | 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 |
| RA | 1,945,772:1 | +C | 4.3% | coding (205/612 nt) | ruvA ← | component of RuvABC resolvasome, regulatory subunit |
| RA | 1,945,772:2 | +T | 4.3% | coding (205/612 nt) | ruvA ← | component of RuvABC resolvasome, regulatory subunit |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,304,796 | T→C | 18.9% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,509,495 | C→G | 100% | intergenic (‑71/‑133) | glk ← / → yfeO | glucokinase/putative ion channel protein |
| RA | 2,639,634 | Δ1 bp | 6.8% | coding (940/1275 nt) | hisS ← | histidyl tRNA synthetase |
| RA | 2,839,669 | A→T | 4.8% | I50F (ATC→TTC) | ascF → | cellobiose/arbutin/salicin‑specific PTS enzymes, IIB and IC components |
| RA | 2,903,483 | T→C | 5.5% | intergenic (+111/+1262) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase, queosine biosynthesis |
| RA | 3,088,093 | T→A | 100% | intergenic (+235/‑189) | metK → / → galP | S‑adenosylmethionine synthetase/D‑galactose transporter |
| RA | 3,240,628 | G→T | 4.8% | V229V (GTG→GTT) | sstT → | sodium:serine/threonine symporter |
| RA | 3,321,017 | C→A | 6.8% | E199* (GAG→TAG) | yhbX ← | putative EptAB family phosphoethanolamine transferase, inner membrane protein |
| RA | 3,493,418 | A→G | 4.9% | M285V (ATG→GTG) | tsgA → | putative transporter |
| RA | 3,510,386 | G→A | 3.3% | L197F (CTT→TTT) | yhfX ← | putative pyridoxal 5'‑phosphate binding protein |
| RA | 3,709,563 | A→T | 4.2% | R304R (CGT→CGA) | eptB ← | KDO phosphoethanolamine transferase, Ca(2+)‑inducible |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,955,249 | T→A | 2.7% | F591L (TTT→TTA) | ilvD → | dihydroxyacid dehydratase |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,203,423 | G→C | 4.2% | A35A (GCG→GCC) | zraR → | fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein |
| RA | 4,293,305 | G→A | 4.1% | Q48Q (CAG→CAA) | nrfF → | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfF |
| RA | 4,296,189 | A→G | 39.6% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 40.1% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 17.8% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,329,420 | T→C | 3.9% | F20F (TTT→TTC) | yjcZ → | YjcZ family protein, yhjH motility defect suppressor |
| RA | 4,410,509 | G→T | 5.6% | E126* (GAA→TAA) | yjfI → | DUF2170 family protein |
| RA | 4,557,269 | C→T | 3.5% | C92C (TGC→TGT) | iraD → | RpoS stabilzer after DNA damage, anti‑RssB factor |
| RA | 4,639,119 | A→T | 4.3% | E314V (GAA→GTA) | creD → | inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533682 | 2536375 | 2694 | 27 [23] | [23] 24 | ptsH–crr | ptsH, ptsI, crr |
| * | * | ÷ | NC_000913 | 3423892–3424403 | 3424403 | 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 | 257908 = | NA (NA) | 60 (0.800) | 50/512 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 39 (0.520) | 24 (0.340) | 22/480 | NT | 43.0% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 27 (0.380) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 38 (0.500) | 44 (0.620) | 34/480 | NT | 58.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 27 (0.380) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 2 (0.030) | 58 (0.770) | 44/512 | NT | 96.7% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 41 (0.540) | 29/512 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 47 (0.620) | 38/512 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2024155 = | 0 (0.000) | 46 (0.610) | 32/512 | NT | 100% | coding (188/624 nt) | rcsA | transcriptional regulator of colanic acid capsular biosynthesis |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 2024158 | 0 (0.000) | 71 (0.940) | 46/512 | NT | 100% | coding (191/624 nt) | rcsA | transcriptional regulator of colanic acid capsular biosynthesis |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 83 (1.100) | 67/512 | NT | 100% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 3526447 = | 0 (0.000) | intergenic (‑300/‑20) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 91 (1.210) | 64/510 | NT | 100% | intergenic (‑31/+2) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| ? | NC_000913 | = 3526451 | 0 (0.000) | intergenic (‑304/‑16) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | 3051050 = | 44 (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 | 3051233 = | 53 (0.740) | coding (1083/1203 nt) | ubiI | 2‑octaprenylphenol hydroxylase, FAD‑dependent | |||||
| * | ? | NC_000913 | 3845530 = | 64 (0.850) | 88 (1.220) | 58/492 | NT | 57.2% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992759 | 70 (0.970) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 4380827 | 56 (0.740) | 3 (0.040) | 3/496 | NT | 3.7% | coding (1493/1809 nt) | frdA | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit |
| ? | NC_000913 | = 4381015 | 101 (1.380) | coding (1305/1809 nt) | frdA | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit | |||||