mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 107,553 | (T)9→8 | intergenic (+79/‑152) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 308,054 | (C)7→6 | coding (1279/2526 nt) | ecpC ← | ECP production outer membrane protein |
| RA | 339,557 | T→C | G411G (GGT→GGC) | yahG → | DUF1116 family protein |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 410,479 | A→G | S112S (TCA→TCG) | mak → | manno(fructo)kinase |
| RA | 460,991 | G→A | A702T (GCA→ACA) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 953,802 | A→G | V222A (GTA→GCA) | focA ← | formate channel |
| RA | 1,143,641 | G→A | H243Y (CAT→TAT) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,246,073 | C→T | G435D (GGC→GAC) | treA ← | periplasmic trehalase |
| RA | 1,489,197 | C→T | D322D (GAC→GAT) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,755,639 | G→A | intergenic (‑498/‑59) | ydhZ ← / → pykF | uncharacterized protein/pyruvate kinase I |
| RA | 1,803,104 | A→G | pseudogene (11/426 nt) | arpB → | pseudogene, ankyrin repeats |
| RA | 1,835,622 | G→A | R36R (CGG→CGA) | ynjA → | carboxymuconolactone decarboxylase family protein |
| RA | 1,868,250 | A→G | Y448C (TAC→TGC) | yeaG → | protein kinase, endogenous substrate unidentified; autokinase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,018,260 | (A)8→7 | coding (315/444 nt) | fliJ → | flagellar protein |
| RA | 2,067,300 | C→T | G8R (GGA→AGA) | insH1 ← | IS5 transposase and trans‑activator |
| 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 | 2,348,753 | Δ1 bp | coding (240/255 nt) | yfaE → | ferredoxin involved with ribonucleotide reductase diferric‑tyrosyl radical (Y*) cofactor maintenance |
| JC | 2,462,889 | (C)9→12 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,470,410 | (T)7→6 | coding (1280/1332 nt) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,516,689 | T→C | T382A (ACG→GCG) | yfeA ← | putative diguanylate cyclase |
| RA | 2,645,886 | (C)5→4 | coding (1440/2313 nt) | pbpC ← | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain protein |
| RA | 2,652,855 | (G)6→7 | coding (362/846 nt) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,731,312 | G→A | intergenic (‑155/+288) | rrsG ← / ← clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone |
| RA | 2,765,794 | (C)7→8 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; RNase LS |
| RA | 2,767,507 | (C)7→8 | intergenic (+152/‑203) | rnlB → / → yfjP | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; 50S ribosome‑binding GTPase family protein |
| RA | 2,809,774 | (T)7→8 | coding (158/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,866,592 | +C | coding (960/993 nt) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,966,582 | C→T | G618D (GGC→GAC) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,008,075 | A→G | D189G (GAC→GGC) | ygeX → | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| RA | 3,184,487 | Δ1 bp | intergenic (‑21/‑353) | ribB ← / → yqiC | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/BMFP family putative fusogenic protein |
| RA | 3,194,516 | A→G | K551K (AAA→AAG) | yqiK → | PHB family membrane protein, function unknown |
| RA | 3,214,605 | G→A | G520E (GGG→GAG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,249,448 | T→C | L25P (CTT→CCT) | yqjD → | membrane‑anchored ribosome‑binding protein |
| RA | 3,304,813 | (C)7→6 | coding (1005/1245 nt) | mtr ← | tryptophan transporter of high affinity |
| RA | 3,352,673 | T→C | E118G (GAA→GGA) | arcB ← | aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| RA | 3,379,266 | (C)7→8 | coding (732/1128 nt) | zapE ← | divisome ATPase |
| RA | 3,397,925 | Δ1 bp | coding (454/594 nt) | yhdE ← | dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo‑UTP pyrophosphatase |
| RA | 3,411,299 | T→C | V10A (GTA→GCA) | fis → | global DNA‑binding transcriptional dual regulator |
| RA | 3,459,293 | (G)5→6 | coding (955/1482 nt) | gspE → | general secretory pathway component, cryptic |
| RA | 3,519,367 | C→T | intergenic (‑303/+98) | aroK ← / ← hofQ | shikimate kinase I/DNA catabolic putative fimbrial transporter |
| RA | 3,525,601 | Δ1 bp | coding (549/561 nt) | nudE ← | adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase |
| 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 |
| MC JC | 3,582,206 | Δ1,222 bp | IS1‑mediated | [yhhZ]–yrhA | [yhhZ], yrhA |
| RA | 3,648,144 | (T)7→6 | intergenic (‑356/‑384) | dinQ ← / → arsR | UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system/arsenical resistance operon transcriptional repressor; autorepressor |
| JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,891,662 | C→T | P16P (CCC→CCT) | mdtL → | multidrug efflux system protein |
| RA | 3,951,598 | +T | pseudogene (57/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,991,301 | C→T | P50L (CCG→CTG) | cyaA → | adenylate cyclase |
| RA | 4,060,280 | (T)9→8 | intergenic (+50/‑167) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,109,928 | (A)7→6 | intergenic (+105/‑2) | sbp → / → cdh | sulfate transporter subunit/CDP‑diacylglycerol phosphotidylhydrolase |
| RA | 4,121,887 | (GC)5→4 | coding (400‑401/531 nt) | hslV ← | peptidase component of the HslUV protease |
| RA | 4,128,359 | C→T | A13T (GCT→ACT) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,215,178 | Δ1 bp | coding (899/930 nt) | metA → | homoserine O‑transsuccinylase |
| RA | 4,296,060 | C→T | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,337,024 | G→A | S3L (TCG→TTG) | adiC ← | arginine:agmatine antiporter |
| RA | 4,397,557 | G→T | G49V (GGT→GTT) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| RA | 4,488,027 | A→G | D237G (GAC→GGC) | lptG → | lipopolysaccharide export ABC permease |
| RA | 4,494,883 | (A)7→8 | coding (261/564 nt) | idnK → | D‑gluconate kinase, thermosensitive |
| RA | 4,573,528 | A→G | pseudogene (1115/1503 nt) | yjiT → | pseudogene |
| RA | 4,638,193 | (C)6→7 | coding (16/1353 nt) | creD → | inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 226074–226299 | 228625–226988 | 690–2552 | 65 [64] | [63] 66 | rrlH | 23S ribosomal RNA of rrnH operon |
| * | * | ÷ | NC_000913 | 3423715–3424234 | 3424595–3424238 | 5–881 | 65 [63] | [64] 66 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3762295–3764074 | 3765216–3764076 | 3–2922 | 65 [64] | [64] 65 | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 7 (0.050) | 114 (1.040) | 79/166 | 0.1 | 93.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 9 (0.080) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 7 (0.050) | 95 (0.870) | 57/166 | 1.1 | 92.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 9 (0.080) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 186 (1.480) | 108/190 | 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 | |||||