mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 101,138 | C→T | A125V (GCC→GTC) | murC → | UDP‑N‑acetylmuramate:L‑alanine ligase |
| RA | 246,960 | A→G | K83K (AAA→AAG) | yafL → | putative lipoprotein and C40 family peptidase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 271,227 | A→G | T209A (ACG→GCG) | insI1 → | IS30 transposase |
| RA | 300,196 | A→G | F247L (TTC→CTC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 323,369 | G→A | V344V (GTG→GTA) | ykgF → | ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 507,927 | T→C | T52A (ACC→GCC) | ybaP ← | TraB family protein |
| MC JC | 575,786 | Δ4,202 bp | IS5‑mediated | [nmpC]–[ybcW] | [nmpC], essD, rrrD, rzpD, rzoD, borD, ybcV, [ybcW] |
| RA | 700,870 | A→G | V242A (GTC→GCC) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 1,055,493 | G→A | A229V (GCA→GTA) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,212,088 | (C)8→7 | intergenic (‑85/+615) | iraM ← / ← ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| RA | 1,529,218 | C→T | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,594,132 | (C)8→7 | pseudogene (3856/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,707,028 | T→C | V37A (GTA→GCA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,830,360 | T→C | N136D (AAC→GAC) | astA ← | arginine succinyltransferase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,048,553 | G→A | G1206S (GGC→AGC) | yeeJ → | putative adhesin |
| 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 | 2,230,157 | G→A | L77L (CTG→TTG) | dusC ← | tRNA‑dihydrouridine synthase C |
| RA | 2,502,577 | G→A | P637S (CCG→TCG) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,687,541 | Δ1 bp | coding (1263/1335 nt) | glrR ← | response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK |
| RA | 2,723,934 | A→G | K403R (AAA→AGA) | pssA → | phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase |
| RA | 2,756,933 | G→A | E259K (GAG→AAG) | intA → | CP4‑57 prophage; integrase |
| RA | 2,757,236 | G→A | A360T (GCG→ACG) | intA → | CP4‑57 prophage; integrase |
| RA | 2,810,153 | Δ1 bp | coding (537/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,958,612 | T→C | E91E (GAA→GAG) | ptrA ← | protease III |
| RA | 2,973,798 | G→A | A22V (GCG→GTG) | lplT ← | lysophospholipid transporter |
| RA | 2,999,680 | (G)7→8 | coding (212/756 nt) | ygeR ← | LysM domain‑containing M23 family putative peptidase; septation lipoprotein |
| RA | 3,102,677 | (A)5→4 | coding (176/720 nt) | trmI ← | tRNA m(7)G46 methyltransferase, SAM‑dependent |
| RA | 3,197,293 | T→C | E783E (GAA→GAG) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,419 | G→A | A408V (GCG→GTG) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,205,882 | T→C | L125L (TTA→TTG) | ttdR ← | transcriptional activator of ttdABT |
| RA | 3,273,187 | G→A | S124F (TCC→TTC) | garL ← | alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase |
| RA | 3,341,408 | G→A | C48Y (TGT→TAT) | kdsD → | D‑arabinose 5‑phosphate isomerase |
| 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 | 3,644,577 | G→A | A202A (GCC→GCT) | prlC ← | oligopeptidase A |
| RA | 3,750,566 | G→A | A161T (GCA→ACA) | sgbE → | L‑ribulose‑5‑phosphate 4‑epimerase |
| RA | 3,815,810 | Δ1 bp | intergenic (‑42/+24) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,853,127 | Δ1 bp | intergenic (‑139/‑426) | ivbL ← / → tisB | ilvB operon leader peptide/toxic membrane persister formation peptide, LexA‑regulated |
| RA | 3,951,559 | +A | pseudogene (18/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 3,987,439 | G→A | A148A (GCC→GCT) | hemY ← | putative protoheme IX synthesis protein |
| RA | 4,187,507 | A→C | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,226,960 | G→A | D1045N (GAC→AAC) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 4,239,245 | (G)5→6 | coding (1612/2097 nt) | yjbH → | DUF940 family extracellular polysaccharide protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| MC JC | 4,397,624 | (GCTGGC)3→2 | coding (213‑218/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,627,743 | C→T | N143N (AAC→AAT) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423710–3424501 | 3424501 | 1–792 | 97 [95] | [96] 98 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 8 (0.050) | 133 (0.810) | 109/566 | 0.4 | 91.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 16 (0.100) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 9 (0.050) | 108 (0.660) | 88/566 | 1.3 | 89.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 16 (0.100) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 206 (1.200) | 158/590 | 0.0 | 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 | |||||