mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| RA | 245,803 | C→T | M1M (ATG→ATA) † | yafK ← | L,D‑transpeptidase‑related protein |
| 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 | 647,740 | +G | coding (296/552 nt) | citX ← | apo‑citrate lyase phosphoribosyl‑dephospho‑CoA transferase |
| RA | 713,788 | C→T | I77I (ATC→ATT) | pgm → | phosphoglucomutase |
| RA | 1,105,536 | A→G | A41A (GCA→GCG) | ymdA → | uncharacterized protein |
| 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 | 1,416,279 | 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 | 1,684,175 | T→C | S432P (TCT→CCT) | rstB → | sensory histidine kinase of RstAB two‑component system |
| RA | 1,814,166 | T→C | R100R (CGT→CGC) | katE → | catalase HPII, heme d‑containing |
| 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 | 2,071,304 | 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 | 2,071,480 | C→T | noncoding (164/195 nt) | isrC → | 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 | 2,313,622 | G→A | W45* (TGG→TGA) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,493,127 | T→C | D43G (GAC→GGC) | frc ← | formyl‑CoA transferase, NAD(P)‑binding |
| RA | 2,504,660 | G→A | P296P (CCC→CCT) | ypdE ← | aminopeptidase |
| RA | 2,505,003 | T→C | H182R (CAC→CGC) | ypdE ← | aminopeptidase |
| 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 | 2,871,308 | G→A | T158I (ACA→ATA) | ispF ← | 2C‑methyl‑D‑erythritol 2,4‑cyclodiphosphate synthase |
| 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 | 2,980,232 | 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 | 3,173,808 | T→A | D530V (GAT→GTT) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| 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 | 3,993,464 | Δ1 bp | coding (2312/2547 nt) | cyaA → | adenylate cyclase |
| 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 | 4,384,861 | G→A | Q341Q (CAG→CAA) | yjeM → | putative transporter |
| RA | 4,429,264 | C→T | N110N (AAC→AAT) | fklB → | FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| RA | 4,476,575 | T→C | V380A (GTA→GCA) | yjgL → | SopA‑central‑domain‑like hexapeptide repeat protein |
| 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 | 433063 | 433112 | 50 | 3 [1] | [2] 6 | nrdR | Nrd regulon repressor |
| * | * | ÷ | NC_000913 | 807316 | 810369 | 3054 | 5 [2] | [2] 4 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2857138 | 2859610 | 2473 | 11 [0] | [2] 3 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3256448 | 3256492 | 45 | 3 [1] | [2] 3 | yhaM | putative L‑serine dehydratase alpha chain |
| * | * | ÷ | NC_000913 | 3423772–3424233 | 3424525–3424238 | 6–754 | 4 [2] | [1] 4 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 274738 | NA (NA) | 3 (0.110) | 3/220 | 2.7 | NA | noncoding (412/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 274760 | NA (NA) | noncoding (390/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 7 (0.250) | 24 (0.990) | 18/192 | 0.3 | 82.8% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 4 (0.170) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 7 (0.250) | 21 (0.870) | 20/192 | 0.2 | 80.8% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 4 (0.170) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||