mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | BS168_reference_genome | 73,935 | T→C | Y43H (TAT→CAT) | prkT → | serine/threonine‑protein kinase |
| RA | BS168_reference_genome | 127,648 | A→G | E696G (GAA→GGA) | rpoC → | RNA polymerase (beta' subunit) |
| RA | BS168_reference_genome | 143,659 | C→T | S100F (TCT→TTT) | rpsE → | ribosomal protein S5 |
| RA | BS168_reference_genome | 165,749 | Δ1 bp | intergenic (+42/‑5) | rrnI‑5S → / → trnI‑Asn | ribosomal RNA‑5S/tRNA‑Asn |
| RA | BS168_reference_genome | 165,751 | Δ1 bp | intergenic (+44/‑3) | rrnI‑5S → / → trnI‑Asn | ribosomal RNA‑5S/tRNA‑Asn |
| RA | BS168_reference_genome | 165,826 | +C | intergenic (+1/‑4) | trnI‑Asn → / → trnI‑Thr | tRNA‑Asn/tRNA‑Thr |
| RA | BS168_reference_genome | 166,037 | +T | intergenic (+4/‑27) | trnI‑Gly → / → trnI‑Arg | tRNA‑Gly/tRNA‑Arg |
| RA | BS168_reference_genome | 166,345 | Δ1 bp | intergenic (+17/‑155) | trnI‑Ala → / → rrnH‑16S | tRNA‑Ala/ribosomal RNA‑16S |
| RA | BS168_reference_genome | 376,025 | (G)8→7 | intergenic (‑227/‑7) | hxlA ← / → hxlR | 3‑hexulose‑6‑phosphate synthase (HPS)/positive regulator of hxlAB expression (formaldehyde sensing) |
| RA | BS168_reference_genome | 506,071 | C→A | P307Q (CCG→CAG) | ydbM → | putative acyl‑CoA dehydrogenase |
| RA | BS168_reference_genome | 557,870 | (T)5→6 | intergenic (+421/‑3) | yddT → / → ydzN | putative exported phage protein/hypothetical protein |
| RA | BS168_reference_genome | 842,292 | A→G | Y569H (TAC→CAC) | ltaSB ← | enzyme responsible for polyglycerolphosphate LTA synthesis |
| RA | BS168_reference_genome | 892,022 | A→T | N196I (AAT→ATT) | malR → | transcriptional activator of the Mal operon |
| RA | BS168_reference_genome | 961,037 | (A)5→6 | intergenic (‑51/‑357) | katA ← / → ssuB | vegetative catalase 1/aliphatic sulfonate ABC transporter (ATP‑binding protein) |
| RA | BS168_reference_genome | 1,073,672 | A→T | F16I (TTC→ATC) | scoC ← | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| RA | BS168_reference_genome | 1,153,146 | C→T | G301G (GGC→GGT) | mblK → | hydrolase/isomerase involved in remodelling the bacterial envelope |
| RA | BS168_reference_genome | 1,317,152 | +GT | intergenic (+23/+5) | phrA → / ← yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| RA | BS168_reference_genome | 1,317,158 | (T)5→6 | coding (257/258 nt) | yjpA ← | putative enzyme |
| RA | BS168_reference_genome | 1,474,890 | C→T | L45L (TTG→TTA) | kre ← | regulator of transcription factor ComK function via modulation of mRNA stability |
| RA | BS168_reference_genome | 1,481,481 | T→C | intergenic (+30/‑66) | ykzU → / → ykuH | conserved hypothetical protein/conserved protein of unknown function |
| RA | BS168_reference_genome | 1,524,173 | T→G | T205P (ACC→CCC) | rnjA ← | ribonuclease J1 |
| RA | BS168_reference_genome | 1,690,759 | G→A | R214H (CGT→CAT) | codY → | transcriptional regulator, GTP and BCAA‑dependent |
| RA | BS168_reference_genome | 2,088,163 | A→G | Q156Q (CAA→CAG) | yocC → | conserved protein of unknown function |
| RA | BS168_reference_genome | 2,097,087 | (A)7→8 | intergenic (‑111/+39) | azoJ ← / ← yocK | FMN‑dependent NADH‑azoreductase/putative general stress protein |
| RA | BS168_reference_genome | 2,271,424 | T→C | R78R (AGA→AGG) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | BS168_reference_genome | 2,271,505 | C→T | V51V (GTG→GTA) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | BS168_reference_genome | 2,271,523 | A→C | D45E (GAT→GAG) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | BS168_reference_genome | 2,291,897 | C→A | E130* (GAG→TAG) | scuA ← | assembly factor BSco of the Cu(A) site of cytochrome c oxidase |
| RA | BS168_reference_genome | 2,387,885 | (A)7→8 | coding (704/735 nt) | yphF ← | putative lipoprotein of unknown function |
| RA | BS168_reference_genome | 2,480,646 | 2 bp→AT | intergenic (+21/+103) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | BS168_reference_genome | 2,480,654 | Δ1 bp | intergenic (+29/+96) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | BS168_reference_genome | 2,480,667 | Δ1 bp | intergenic (+42/+83) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | BS168_reference_genome | 2,581,732 | (T)6→7 | intergenic (‑115/+39) | pstS ← / ← pbpA | phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
| RA | BS168_reference_genome | 2,861,836 | (A)9→8 | intergenic (‑88/+4) | mreB ← / ← ysxA | cell‑shape determining protein/conserved nucleotide‑related metabolism protein |
| RA | BS168_reference_genome | 2,992,352 | C→T | L755L (TTG→TTA) | dnaEC ← | DNA polymerase III (alpha subunit), DnaE3 |
| RA | BS168_reference_genome | 3,770,066 | (A)8→9 | intergenic (‑258/+38) | ywzF ← / ← csbD | conserved protein of unknown function/stress response protein |
| RA | BS168_reference_genome | 3,935,825 | Δ1 bp | coding (1190/1191 nt) | rlmI ← | large subunit ribosomal RNA m5C1962 methyltransferase |
| RA | BS168_reference_genome | 4,124,455 | T→C | Y163C (TAT→TGT) | liaM ← | permease for export of regulatory peptide LiaD* |
| RA | BS168_reference_genome | 4,153,115 | G→T | L192I (CTT→ATT) | walK ← | two‑component sensor histidine kinase [YycG] |
| RA | BS168_reference_genome | 4,155,395 | (A)5→6 | intergenic (‑186/+38) | trnY‑Lys ← / ← purA | tRNA‑Lys/adenylosuccinate synthetase |
| RA | pSIJ663_pHT315_araE_xy | 2,655 | Δ3 bp | intergenic (–/‑321) | – / → eryR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 3,843 | Δ5 bp | intergenic (+128/‑24) | eryR → / → ampR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 5,049 | C→T | intergenic (+318/–) | ampR → / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | BS168_reference_genome | 160970–164866 | 165598–164903 | 38–4629 | 21 [20] | [15] 22 | [rrnI‑16S]–[rrnI‑5S] | [rrnI‑16S],rrnI‑23S,[rrnI‑5S] |
| * | * | ÷ | BS168_reference_genome | 166437–166702 | 171227–170021 | 3320–4791 | 21 [20] | [20] 25 | rrnH‑16S–[rrnH‑5S] | rrnH‑16S,rrnH‑23S,[rrnH‑5S] |
| * | * | ÷ | BS168_reference_genome | 171469–171677 | 176229–172977 | 1301–4761 | 21 [20] | [20] 21 | rrnG‑16S–[rrnG‑5S] | rrnG‑16S,rrnG‑23S,[rrnG‑5S] |
| * | * | ÷ | BS168_reference_genome | 202107 | 202126 | 20 | 22 [20] | [18] 21 | [ybbU] | [ybbU] |
| * | * | ÷ | BS168_reference_genome | 3484177–3485465 | 3486761 | 1297–2585 | 21 [19] | [0] 48 | [araE]–araR | [araE],araR |
| * | * | ÷ | pSIJ663_pHT315_araE_xy | 6326 | 6416 | 91 | 4 [2] | [3] 4 | ampR/– | –/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | BS168_reference_genome | 2410998 = | 72 (0.780) | 48 (0.540) | 24/244 | 1.8 | 57.7% | intergenic (‑409/‑88) | fmnP/serA | FMN permease/3‑phosphoglycerate dehydrogenase |
| ? | BS168_reference_genome | 3486762 = | 0 (0.000) | intergenic (+4/+45) | araR/yvbT | transcriptional repressor of the ara regulon (LacI family)/putative alkanal monooxygenase | |||||
| * | ? | BS168_reference_genome | = 2411050 | 70 (0.760) | 59 (0.950) | 25/250 | 1.7 | 45.7% | intergenic (‑461/‑36) | fmnP/serA | FMN permease/3‑phosphoglycerate dehydrogenase |
| ? | pSIJ663_pHT315_araE_xy | 9781 = | NA (NA) | intergenic (+5050/–) | ampR/– | –/– | |||||