mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 149,436 | A→G | 7.0% | S56P (TCC→CCC) | panB ← | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 272,636 | T→G | 20.2% | noncoding (57/75 nt) | eyeA → | novel sRNA, function unknown, CP4‑6 propahge |
| RA | 404,848 | A→G | 14.9% | L266P (CTC→CCC) | proC ← | pyrroline‑5‑carboxylate reductase, NAD(P)‑binding |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 100% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 507,782 | T→G | 25.0% | H100P (CAC→CCC) | ybaP ← | TraB family protein |
| RA | 729,603 | G→C | 14.0% | A7A (GCG→GCC) | rhsC → | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 1,058,486 | T→C | 15.5% | S135P (TCG→CCG) | torC → | trimethylamine N‑oxide (TMAO) reductase I, cytochrome c‑type subunit |
| RA | 1,186,332 | T→G | 18.1% | G163G (GGT→GGG) | pepT → | peptidase T |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,400,230 | T→C | 17.5% | R3G (AGA→GGA) | ogt ← | O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| RA | 1,424,240 | G→T | 32.9% | L153F (TTG→TTT) | trkG → | Rac prophage; potassium transporter subunit |
| RA | 1,520,084 | G→A | 32.9% | intergenic (+20/‑178) | curA → / → mcbR | curcumin/dihydrocurcumin reductase, NADPH‑dependent/colanic acid and biofilm gene transcriptional regulator, MqsR‑controlled |
| RA | 1,663,858 | A→G | 14.8% | S84G (AGT→GGT) | ynfH → | oxidoreductase, membrane subunit |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,321,743 | T→A | 7.3% | G567G (GGT→GGA) | atoS → | sensory histidine kinase in two‑component regulatory system with AtoC |
| RA | 2,354,500 | T→C | 18.6% | L79P (CTC→CCC) | glpB → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase membrane anchor subunit |
| RA | 2,411,025 | T→C | 13.1% | S110G (AGT→GGT) | yfbS ← | putative transporter |
| RA | 2,550,538 | Δ1 bp | 5.8% | coding (8/900 nt) | yfeX ← | porphyrinogen oxidase, cytoplasmic |
| RA | 2,913,613 | A→C | 15.3% | G13G (GGT→GGG) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,934,874 | Δ1 bp | 8.7% | coding (640/1317 nt) | fucP → | L‑fucose transporter |
| RA | 3,154,407 | A→T | 9.8% | I271N (ATC→AAC) | yqhC ← | transcriptional activator of yqhD |
| RA | 3,210,861 | T→G | 21.3% | G27G (GGT→GGG) | rpsU → | 30S ribosomal subunit protein S21 |
| RA | 3,217,530 | T→C | 23.6% | intergenic (+128/+26) | yqjI → / ← aer | PadR family putative transcriptional regulator/fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,398,941 | A→G | 28.3% | S346S (TCT→TCC) | mreC ← | cell wall structural complex MreBCD transmembrane component MreC |
| RA | 3,489,443 | Δ1 bp | 6.4% | coding (738/1221 nt) | argD ← | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase |
| RA | 3,560,455:1 | +G | 100% | 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 | 3,728,950 | T→C | 15.1% | E141G (GAG→GGG) | xylB ← | xylulokinase |
| RA | 3,809,086 | C→A | 9.3% | Q183K (CAA→AAA) | waaA → | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase) |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,862,956 | G→A | 19.3% | pseudogene (648/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| JC | 4,001,645 | Δ5 bp | 93.9% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,163,578 | T→C | 6.7% | intergenic (‑308/‑61) | trmA ← / → btuB | tRNA m(5)U54 methyltransferase, SAM‑dependent; tmRNA m(5)U341 methyltransferase/vitamin B12/cobalamin outer membrane transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,304,821 | T→C | 6.6% | N593D (AAC→GAC) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 357779 | 357960 | 182 | 10 [9] | [9] 10 | [cynR] | [cynR] |
| * | * | ÷ | NC_000913 | 583380 | 583656 | 277 | 10 [9] | [9] 10 | tfaX/appY | pseudogene, DLP12 prophage;Phage or Prophage Related/global transcriptional activator; DLP12 prophage |
| * | * | ÷ | NC_000913 | 720924 | 721083 | 160 | 10 [9] | [9] 10 | [kdpE] | [kdpE] |
| * | * | ÷ | NC_000913 | 1212022 | 1212293 | 272 | 12 [8] | [9] 10 | iraM/ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| * | * | ÷ | NC_000913 | 1640961 | 1641038 | 78 | 10 [8] | [9] 10 | essQ/cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock protein |
| * | * | ÷ | NC_000913 | 2470137 | 2470400 | 264 | 11 [8] | [9] 11 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 3423855–3424232 | 3424435–3424239 | 8–581 | 10 [9] | [8] 10 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3799021 | 3799498 | 478 | 10 [9] | [9] 10 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 3804742 | 3805115 | 374 | 13 [9] | [8] 10 | waaS | lipopolysaccharide rhamnose:KdoIII transferase; lipopolysaccharide core biosynthesis protein |
| * | * | ÷ | NC_000913 | 4233766 | 4235397 | 1632 | 10 [9] | [8] 10 | pgi | glucosephosphate isomerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 13 (0.260) | 48 (1.050) | 36/376 | NT | 84.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 6 (0.130) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 12 (0.240) | 49 (1.080) | 41/376 | NT | 85.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 6 (0.130) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 24 (0.500) | 18/400 | NT | 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 | |||||