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 |
| RA | 220,849 | (T)5→4 | coding (80/816 nt) | metQ ← | DL‑methionine transporter subunit |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 349,717 | T→C | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 379,603 | C→T | intergenic (‑32/+3) | frmA ← / ← frmR | alcohol dehydrogenase class III; glutathione‑dependent formaldehyde dehydrogenase/regulator protein that represses frmRAB operon |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+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 | 460,326 | C→T | P480L (CCG→CTG) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 740,004 | G→A | M166I (ATG→ATA) | phr → | deoxyribodipyrimidine photolyase, FAD‑binding |
| 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 | 1,156,112 | T→C | A117A (GCT→GCC) | holB → | DNA polymerase III, delta prime subunit |
| RA | 1,246,073 | C→T | G435D (GGC→GAC) | treA ← | periplasmic trehalase |
| RA | 1,409,250 | (T)8→9 | intergenic (+217/‑261) | ydaN → / → dbpA | putative Zn(II) transporter/ATP‑dependent RNA helicase, specific for 23S rRNA |
| RA | 1,489,197 | C→T | D322D (GAC→GAT) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,597,313 | (C)7→8 | pseudogene (675/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,755,639 | G→A | intergenic (‑498/‑59) | ydhZ ← / → pykF | uncharacterized protein/pyruvate kinase I |
| 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 | 2,173,363 | 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 | 2,202,110 | T→C | F611S (TTT→TCT) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,304,221 | C→T | A106V (GCC→GTC) | eco → | ecotin, a serine protease inhibitor |
| 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 | 2,652,855 | (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 | 2,790,586 | T→C | L202P (CTG→CCG) | lhgO → | L‑2‑hydroxyglutarate oxidase |
| RA | 2,809,774 | (T)7→8 | coding (158/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,856,887 | C→T | intergenic (‑81/‑206) | ygbA ← / → mutS | uncharacterized protein/methyl‑directed mismatch repair protein |
| RA | 2,866,592 | +C | coding (960/993 nt) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,967,887 | G→A | A183V (GCC→GTC) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,007,187 | A→T | D309V (GAC→GTC) | ygeW → | putative carbamoyltransferase |
| RA | 3,008,075 | A→G | D189G (GAC→GGC) | ygeX → | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| RA | 3,194,516 | A→G | K551K (AAA→AAG) | yqiK → | PHB family membrane protein, function unknown |
| RA | 3,249,628 | G→A | G85D (GGC→GAC) | yqjD → | membrane‑anchored ribosome‑binding protein |
| RA | 3,298,809 | A→G | V13A (GTG→GCG) | yraR ← | putative nucleoside‑diphosphate‑sugar epimerase |
| 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 | 3,411,299 | T→C | V10A (GTA→GCA) | fis → | global DNA‑binding transcriptional dual regulator |
| RA | 3,520,513 | T→C | D64G (GAT→GGT) | hofQ ← | DNA catabolic putative fimbrial transporter |
| RA | 3,549,792 | (C)6→5 | coding (279/2085 nt) | malQ ← | 4‑alpha‑glucanotransferase (amylomaltase) |
| 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 | 3,639,879 | (T)8→7 | intergenic (‑159/‑232) | uspB ← / → uspA | universal stress (ethanol tolerance) protein B/universal stress global response regulator |
| RA | 3,646,678 | G→A | G127D (GGC→GAC) | gor → | glutathione oxidoreductase |
| 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 |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,903,585 | G→A | G39G (GGC→GGT) | bglB ← | cryptic phospho‑beta‑glucosidase B |
| 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 | 4,128,197 | T→C | T67A (ACC→GCC) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,214,649 | A→T | I124F (ATC→TTC) | metA → | homoserine O‑transsuccinylase |
| RA | 4,243,370 | C→T | L49L (CTG→CTA) | malG ← | maltose transporter subunit |
| RA | 4,267,564 | T→C | Y151H (TAT→CAT) | tyrB → | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| RA | 4,295,744 | G→A | A422T (GCT→ACT) | gltP → | glutamate/aspartate:proton symporter |
| 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 | 4,326,047 | C→T | intergenic (‑306/+352) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family 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 | 4,432,376 | (G)5→4 | coding (681/966 nt) | ytfF ← | DMT transporter family inner membrane protein |
| RA | 4,494,883 | (A)7→8 | coding (261/564 nt) | idnK → | D‑gluconate kinase, thermosensitive |
| RA | 4,551,608 | G→A | intergenic (‑312/‑28) | gntP ← / → uxuA | fructuronate transporter/mannonate hydrolase |
| 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 | 3423714–3424234 | 3424592–3424238 | 5–879 | 49 [47] | [46] 49 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3621152–3622298 | 3622644–3622421 | 124–1493 | 52 [48] | [48] 49 | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | * | ÷ | NC_000913 | 3762295–3764074 | 3765225–3764076 | 3–2931 | 49 [48] | [48] 51 | 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 | = 1299498 | 0 (0.000) | 169 (1.610) | 98/190 | 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 | |||||
| * | ? | NC_000913 | 4325861 = | 106 (0.970) | 184 (2.230) | 91/150 | 0.0 | 67.9% | noncoding (60/583 nt) | REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913 | = 4374507 | 94 (1.140) | noncoding (10/99 nt) | RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||