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 |
| RA | 34,120 | (T)9→8 | intergenic (+82/‑180) | carB → / → caiF | carbamoyl‑phosphate synthase large subunit/cai operon transcriptional activator |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 350,431 | G→A | L140L (CTG→CTA) | prpC → | 2‑methylcitrate synthase |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 839,332 | C→T | V734I (GTC→ATC) | fiu ← | catecholate siderophore receptor |
| RA | 925,899 | (G)7→8 | noncoding (73/88 nt) | serW ← | tRNA‑Ser |
| RA | 1,151,929 | G→A | intergenic (+78/‑10) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,393,315 | T→C | V30A (GTA→GCA) | mppA → | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| RA | 1,416,279 | A→G | S370P (TCC→CCC) | recE ← | Rac prophage, exonuclease VIII, 5' to 3' specific dsDNA exonuclease |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,670,695 | A→G | M333V (ATG→GTG) | ynfM → | putative arabinose efflux transporter |
| RA | 1,684,175 | T→C | S432P (TCT→CCT) | rstB → | sensory histidine kinase of RstAB two‑component system |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide and tripeptide permease A/glutathionine S‑transferase |
| RA | 1,715,061 | T→C | K277E (AAA→GAA) | pdxY ← | pyridoxamine kinase |
| RA | 1,718,641 | G→A | A321V (GCC→GTC) | anmK ← | anhydro‑N‑acetylmuramic acid kinase |
| RA | 1,756,374 | G→A | G226D (GGC→GAC) | 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 | 2,061,729 | G→A | R69W (CGG→TGG) | nac ← | nitrogen assimilation regulon transcriptional regulator, autorepressor |
| 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 | 2,073,151 | T→C | L538P (CTG→CCG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,092,066 | G→A | G324S (GGC→AGC) | hisD → | bifunctional histidinal dehydrogenase/ histidinol dehydrogenase |
| 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 | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,250,031 | C→T | I105I (ATC→ATT) | yeiH → | UPF0324 family inner membrane protein |
| RA | 2,391,193 | A→G | F105L (TTC→CTC) | nuoN ← | NADH:ubiquinone oxidoreductase, membrane subunit N |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,504,660 | G→A | P296P (CCC→CCT) | ypdE ← | aminopeptidase |
| RA | 2,505,003 | T→C | H182R (CAC→CGC) | ypdE ← | aminopeptidase |
| RA | 2,542,393 | G→A | A40A (GCC→GCT) | cysU ← | sulfate/thiosulfate ABC transporter permease |
| RA | 2,620,907 | (A)8→9 | intergenic (‑35/‑290) | upp ← / → purM | uracil phosphoribosyltransferase/phosphoribosylaminoimidazole synthetase |
| RA | 2,706,066 | T→C | E353E (GAA→GAG) | lepA ← | back‑translocating elongation factor EF4, GTPase |
| RA | 2,733,223 | G→A | D317D (GAC→GAT) | clpB ← | protein disaggregation chaperone |
| RA | 2,744,303 | A→G | T76T (ACT→ACC) | rplS ← | 50S ribosomal subunit protein L19 |
| RA | 2,759,929 | T→C | H315H (CAT→CAC) | yfjI → | CP4‑57 prophage, uncharacterized protein |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,874,741 | T→C | T227A (ACA→GCA) | cysN ← | sulfate adenylyltransferase, subunit 1 |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 2,947,466 | Δ1 bp | intergenic (+3/‑31) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 2,980,232 | C→T | R135H (CGC→CAC) | ygeA ← | Asp/Glu_racemase family protein |
| RA | 3,032,253 | G→A | R296H (CGT→CAT) | uacT → | uric acid permease |
| 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 | 3,306,716 | C→T | R382H (CGC→CAC) | deaD ← | ATP‑dependent RNA helicase |
| RA | 3,349,840 | T→C | K207R (AAG→AGG) | elbB ← | isoprenoid biosynthesis protein with amidotransferase‑like domain |
| 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 | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | 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 | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 3,971,307 | G→A | L16L (CTG→CTA) | wecC → | UDP‑N‑acetyl‑D‑mannosaminuronic acid dehydrogenase |
| RA | 4,182,817 | A→G | T525A (ACG→GCG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,182,907 | T→C | Y555H (TAC→CAC) | 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 | 4,487,041 | C→T | T275I (ACC→ATC) | lptF → | lipopolysaccharide export ABC permease |
| 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 | 4,567,574 | T→C | T316A (ACC→GCC) | mdtM ← | multidrug efflux system protein |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 433036 | 433102 | 67 | 6 [3] | [4] 5 | nrdR | Nrd regulon repressor |
| * | * | ÷ | NC_000913 | 807330 | 810368 | 3039 | 5 [4] | [3] 7 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 1168896 | 1168993 | 98 | 8 [2] | [4] 5 | ycfQ/bhsA | repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein |
| * | * | ÷ | NC_000913 | 1465136 | 1465224 | 89 | 5 [4] | [4] 6 | [ynbG] | [ynbG] |
| * | * | ÷ | NC_000913 | 1524515 | 1524574 | 60 | 5 [4] | [3] 5 | ansP | L‑asparagine transporter |
| * | * | ÷ | NC_000913 | 1893790 | 1893859 | 70 | 6 [4] | [4] 8 | yoaB/yoaC | putative reactive intermediate deaminase/DUF1889 family protein |
| * | * | ÷ | NC_000913 | 1996867 | 1996926 | 60 | 6 [4] | [3] 8 | sdiA/yecC | quorum‑sensing transcriptional activator/putative ABC transporter ATPase |
| * | * | ÷ | NC_000913 | 2033835 | 2033941 | 107 | 7 [3] | [4] 6 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology, putative outer membrane protein |
| * | * | ÷ | NC_000913 | 2249629 | 2249663 | 35 | 6 [4] | [3] 5 | yeiE/yeiH | putative DNA‑binding transcriptional regulator/UPF0324 family inner membrane protein |
| * | * | ÷ | NC_000913 | 2306830 | 2306883 | 54 | 7 [4] | [1] 5 | mqo/yojI | malate dehydrogenase, FAD/NAD(P)‑binding domain/microcin J25 efflux ABC transporter permease/ATPase |
| * | * | ÷ | NC_000913 | 2857130 | 2859637 | 2508 | 8 [4] | [4] 6 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3275024 | 3275080 | 57 | 6 [4] | [3] 5 | garP/garD | putative (D)‑galactarate transporter/D‑galactarate dehydrogenase |
| * | * | ÷ | NC_000913 | 3423765–3424233 | 3424525–3424241 | 9–761 | 5 [4] | [3] 5 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 4086970 | 4086984 | 15 | 7 [4] | [4] 6 | fdhD/yiiG | formate dehydrogenase formation protein/DUF3829 family lipoprotein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 39 (1.250) | 8 (0.300) | 8/184 | 1.5 | 20.4% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 29 (1.090) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||