mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.1 revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 367,852 | (GC)6→5 | coding (568‑569/834 nt) | mhpR ← | mhp operon transcriptional activator |
| RA | 420,175 | G→A | L195L (CTG→CTA) | brnQ → | branched‑chain amino acid transport system 2 carrier protein, LIV‑II transport system for Ile, Leu, and Val |
| RA | 459,628 | G→A | A247A (GCG→GCA) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 584,639 | C→T | intergenic (+209/+41) | appY → / ← ompT | global transcriptional activator, DLP12 prophage/DLP12 prophage, outer membrane protease VII, outer membrane protein 3b |
| RA | 731,913 | A→G | A777A (GCA→GCG) | rhsC → | Rhs protein with putative toxin domain, putative neighboring cell growth inhibitor |
| RA | 731,919 | A→G | G779G (GGA→GGG) | rhsC → | Rhs protein with putative toxin domain, putative neighboring cell growth inhibitor |
| RA | 752,402 | (T)5→4 | coding (394/567 nt) | ybgD ← | putative fimbrial‑like adhesin protein |
| RA | 1,170,493 | (G)5→6 | intergenic (‑119/+25) | ldtC ← / ← mfd | L,D‑transpeptidase linking Lpp to murein/transcription‑repair coupling factor |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,437,231 | (T)9→8 | intergenic (+2/+29) | micC → / ← pfo | sRNA antisense regulator of OmpC translation, Hfq‑dependent/pyruvate‑flavodoxin oxidoreductase |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,481,041 | A→G | T45A (ACG→GCG) | ynbD → | putative phosphatase inner membrane protein |
| RA | 1,571,850 | T→C | T66A (ACC→GCC) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| RA | 1,594,256 | (C)8→9 | pseudogene (3732/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,629,913 | G→A | P334L (CCG→CTG) | ydfI ← | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,735,897 | T→C | Y174H (TAT→CAT) | sodB → | superoxide dismutase, Fe |
| RA | 1,756,910 | (A)6→5 | coding (1213/1413 nt) | pykF → | pyruvate kinase I |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,027,398 | C→T | W207* (TGG→TAG) | yedQ ← | putative membrane‑anchored diguanylate cyclase |
| RA | 2,071,304 | A→G | intergenic (+93/‑13) | yeeP → / → isrC | pseudogene, CP4‑44 prophage, 50S ribosome‑binding GTPase family,Phage or Prophage Related, putative histone/novel sRNA, CP4‑44, putative prophage remnant |
| RA | 2,073,282 | G→A | G582R (GGA→AGA) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC |
| RA | 2,184,452 | G→A | A22V (GCC→GTC) | thiD ← | hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,335,018 | G→A | L543L (CTG→TTG) | yfaA ← | DUF2138 family protein, putative host defense protein |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,649,905 | G→A | P795S (CCG→TCG) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,697,352 | A→G | N518D (AAT→GAT) | mltF → | membrane‑bound lytic transglycosylase F, murein hydrolase |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,765,666 | T→C | T37T (ACA→ACG) | yfjM ← | CP4‑57 prophage, uncharacterized protein |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,846,715 | T→C | Q233R (CAG→CGG) | hycD ← | hydrogenase 3, membrane subunit |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 2,984,271 | A→G | intergenic (‑147/+140) | kduI ← / ← yqeF | hexuronate isomerase/short chain acyltransferase |
| RA | 3,099,504 | G→A | A21V (GCA→GTA) | yggM ← | DUF1202 family putative secreted protein |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,560,455 | +G | 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 |
| RA | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,811 | C→T | intergenic (‑43/+23) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,901,765 | G→A | G152G (GGC→GGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,902,316 | (T)8→7 | coding (1386/1413 nt) | bglB ← | cryptic phospho‑beta‑glucosidase B |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 3,938,533 | C→T | R103W (CGG→TGG) | rbsR → | transcriptional repressor of ribose metabolism |
| RA | 4,182,791 | A→G | D516G (GAC→GGC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,351,093 | G→A | G190G (GGC→GGT) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,490,935 | A→G | L69L (TTG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,538,491 | C→T | G92D (GGC→GAC) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| RA | 4,621,471 | G→A | A197T (GCC→ACC) | deoD → | purine nucleoside phosphorylase 1, nicotinamide 1‑beta‑D‑riboside phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 731163–731205 | 731886 | 682–724 | 9 [5] | [6] 7 | rhsC | Rhs protein with putative toxin domain, putative neighboring cell growth inhibitor |
| * | * | ÷ | NC_000913 | 732045–732285 | 732502–732344 | 60–458 | 8 [6] | [6] 7 | rhsC | Rhs protein with putative toxin domain, putative neighboring cell growth inhibitor |
| * | * | ÷ | NC_000913 | 807330 | 810364 | 3035 | 7 [6] | [6] 10 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2033829 | 2033927 | 99 | 8 [6] | [4] 8 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology, putative outer membrane protein |
| * | * | ÷ | NC_000913 | 2857134 | 2859609 | 2476 | 8 [5] | [6] 8 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 2995162 | 2995236 | 75 | 7 [6] | [5] 7 | ygeK/ygeN | pseudogene, response regulator family, part of T3SS PAI ETT2 remnant, putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant |
| * | * | ÷ | NC_000913 | 3423749–3424234 | 3424539–3424241 | 8–791 | 10 [6] | [6] 7 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 51 (1.410) | 21 (0.690) | 16/176 | 0.8 | 35.5% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 33 (1.080) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 41 (1.180) | 33/200 | 0.1 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||