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 | 60,432 | G→A | Q945* (CAG→TAG) | rapA ← | RNA polymerase remodeling/recycling factor ATPase, RNA polymerase‑associated, ATP‑dependent RNA translocase |
| RA | 73,762 | A→G | C254R (TGC→CGC) | thiP ← | thiamine/thiamine pyrophosphate ABC transporter permease |
| RA | 238,929 | T→C | pseudogene (174/357 nt) | yafU ← | pseudogene |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 352,986 | A→G | N94S (AAC→AGC) | prpE → | propionate‑‑CoA ligase |
| RA | 371,588 | (G)6→7 | coding (350/867 nt) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase |
| RA | 449,399 | A→G | F415L (TTC→CTC) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 751,737 | (G)6→7 | coding (433/2448 nt) | ybgQ ← | putative outer membrane protein |
| RA | 783,866 | C→T | S234L (TCA→TTA) | pnuC → | nicotinamide riboside transporter |
| RA | 917,894 | A→G | E474E (GAA→GAG) | ybjD → | putative OLD family ATP‑dependent endonuclease, DUF2813 family protein |
| RA | 1,121,934 | A→G | I225T (ATC→ACC) | pyrC ← | dihydro‑orotase |
| RA | 1,190,263 | A→G | L62P (CTG→CCG) | phoP ← | response regulator in two‑component regulatory system with PhoQ |
| 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 | 1,385,656 | A→G | E49G (GAG→GGG) | ycjF → | UPF0283 family inner membrane protein |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| JC JC | 1,491,119 | IS5 (+) +4 bp | coding (218‑221/531 nt) | cybB → | cytochrome b561 |
| RA | 1,581,323 | G→A | T401I (ACA→ATA) | ydeN ← | putative Ser‑type periplasmic non‑aryl sulfatase |
| RA | 1,594,132 | (C)8→9 | pseudogene (3856/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,621,054 | A→G | H28H (CAT→CAC) | eamA ← | cysteine and O‑acetyl‑L‑serine efflux system |
| RA | 1,756,464 | T→C | V256A (GTT→GCT) | 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 | 2,073,094 | T→C | L519P (CTG→CCG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,165,366 | (A)7→6 | coding (178/333 nt) | yegP → | UPF0339 family protein |
| 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 | 2,311,756 | A→G | S332P (TCC→CCC) | ompC ← | outer membrane porin protein C |
| RA | 2,318,281 | T→C | E532E (GAA→GAG) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,319,725 | T→C | E51G (GAA→GGA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,367,989 | (C)5→6 | coding (919/969 nt) | arnC → | undecaprenyl phosphate‑L‑Ara4FN transferase |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,471,819 | A→G | pseudogene (304/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage,Phage or Prophage Related |
| RA | 2,472,769 | T→C | Q38R (CAG→CGG) | yfdN ← | CPS‑53 (KpLE1) prophage, uncharacterized protein |
| RA | 2,523,413 | T→C | T191T (ACA→ACG) | xapB ← | xanthosine transporter |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4, membrane subunit |
| RA | 2,657,358 | G→A | A526A (GCC→GCT) | hscA ← | DnaK‑like molecular chaperone specific for IscU |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,768,876 | G→A | R71Q (CGG→CAG) | yfjQ → | CP4‑57 prophage, uncharacterized protein |
| RA | 2,786,768 | C→T | pseudogene (372/2253 nt) | ygaQ → | uncharacterized protein, putative enzyme |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,159,844 | G→A | P435S (CCA→TCA) | ygiQ ← | Radical SAM superfamily protein |
| RA | 3,216,464 | G→A | R10C (CGC→TGC) | yqjH ← | putative siderophore interacting protein |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,304,827 | C→T | A331T (GCC→ACC) | mtr ← | tryptophan transporter of high affinity |
| 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 | 3,748,181 | G→A | A366A (GCG→GCA) | lyxK → | L‑xylulose kinase |
| 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 | 4,131,253 | G→A | W473* (TGG→TGA) | metL → | Bifunctional aspartokinase/homoserine dehydrogenase 2 |
| 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 | 4,493,661 | A→G | V249A (GTG→GCG) | idnD ← | L‑idonate 5‑dehydrogenase, NAD‑binding |
| RA | 4,538,491 | C→T | G92D (GGC→GAC) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,553,049 | A→G | D50G (GAC→GGC) | uxuB → | D‑mannonate oxidoreductase, NAD‑dependent |
| 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 | 781443 | 781603–781583 | 141–161 | 6 [2] | [5] 7 | [lysZ]–[lysQ] | [lysZ], [lysQ] |
| * | * | ÷ | NC_000913 | 807335 | 810368 | 3034 | 6 [4] | [4] 6 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2857124 | 2859628 | 2505 | 7 [5] | [5] 7 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423732–3424230 | 3424525–3424240 | 11–794 | 7 [5] | [5] 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 = | 30 (0.810) | 11 (0.350) | 11/194 | 1.3 | 31.5% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 22 (0.690) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||