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 | freq | annotation | gene | description |
| RA | BS168_reference_genome | 143,659 | C→T | 100% | S100F (TCT→TTT) | rpsE → | ribosomal protein S5 |
| RA | BS168_reference_genome | 165,749 | Δ1 bp | 100% | intergenic (+42/‑5) | rrnI‑5S → / → trnI‑Asn | ribosomal RNA‑5S/tRNA‑Asn |
| RA | BS168_reference_genome | 165,751 | Δ1 bp | 100% | intergenic (+44/‑3) | rrnI‑5S → / → trnI‑Asn | ribosomal RNA‑5S/tRNA‑Asn |
| RA | BS168_reference_genome | 165,825:1 | +C | 100% | noncoding (72/72 nt) | trnI‑Asn → | tRNA‑Asn |
| RA | BS168_reference_genome | 166,037:1 | +T | 100% | intergenic (+4/‑27) | trnI‑Gly → / → trnI‑Arg | tRNA‑Gly/tRNA‑Arg |
| RA | BS168_reference_genome | 166,344 | Δ1 bp | 100% | intergenic (+16/‑156) | trnI‑Ala → / → rrnH‑16S | tRNA‑Ala/ribosomal RNA‑16S |
| RA | BS168_reference_genome | 376,018 | Δ1 bp | 100% | intergenic (‑220/‑14) | hxlA ← / → hxlR | 3‑hexulose‑6‑phosphate synthase (HPS)/positive regulator of hxlAB expression (formaldehyde sensing) |
| RA | BS168_reference_genome | 557,865:1 | +T | 100% | intergenic (+416/‑8) | yddT → / → ydzN | putative exported phage protein/hypothetical protein |
| RA | BS168_reference_genome | 608,214:1 | +A | 100% | intergenic (‑139/+32) | ydgF ← / ← dinB | putative amino acid permease/nuclease inhibitor |
| RA | BS168_reference_genome | 665,476 | C→T | 6.8% | E597K (GAA→AAA) | gutR ← | transcriptional regulator of the glucitol operon |
| RA | BS168_reference_genome | 892,022 | A→T | 100% | N196I (AAT→ATT) | malR → | transcriptional activator of the Mal operon |
| RA | BS168_reference_genome | 944,526 | A→G | 32.4% | K14E (AAG→GAG) | perR → | transcriptional regulator (Fur family) |
| RA | BS168_reference_genome | 944,551 | C→T | 34.9% | P22L (CCT→CTT) | perR → | transcriptional regulator (Fur family) |
| RA | BS168_reference_genome | 944,586 | T→C | 20.8% | S34P (TCT→CCT) | perR → | transcriptional regulator (Fur family) |
| RA | BS168_reference_genome | 953,306 | C→A | 7.7% | intergenic (+12/+67) | leuTB → / ← spo0M | tRNA‑Leu/protein involved in the control of the cell cycle as a function of the environment |
| RA | BS168_reference_genome | 1,010,959 | C→A | 7.5% | P172H (CCC→CAC) | azr → | oxidoreductase, NAD(P)H‑FMN and ferric iron reductase (azoreductase) |
| RA | BS168_reference_genome | 1,073,040 | C→T | 8.6% | A91A (GCC→GCT) | yhaI → | conserved protein of unknown function |
| RA | BS168_reference_genome | 1,073,489 | C→T | 9.5% | A77T (GCA→ACA) | scoC ← | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| RA | BS168_reference_genome | 1,073,527 | G→C | 37.1% | S64C (TCT→TGT) | scoC ← | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| RA | BS168_reference_genome | 1,074,835 | C→T | 9.4% | G110G (GGG→GGA) | trpP ← | tryptophan transporter or sensor |
| RA | BS168_reference_genome | 1,080,726 | A→G | 6.1% | A205A (GCT→GCC) | sndC ← | N‑acetyl amino acid acetylase, promiscuous activity |
| RA | BS168_reference_genome | 1,164,050 | C→G | 5.2% | S301R (AGC→AGG) | iolQ → | transcriptional repressor of iolX (LacI family) |
| RA | BS168_reference_genome | 1,224,521 | A→G | 36.8% | E356G (GAA→GGA) | oppD → | oligopeptide ABC transporter (ATP‑binding protein) |
| RA | BS168_reference_genome | 1,253,222 | C→T | 7.3% | L40L (CTC→CTT) | yjcZ → | putative type I toxin |
| RA | BS168_reference_genome | 1,317,152:1 | +G | 100% | intergenic (+23/+5) | phrA → / ← yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| RA | BS168_reference_genome | 1,317,152:2 | +T | 90.6% | intergenic (+23/+5) | phrA → / ← yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| RA | BS168_reference_genome | 1,317,153 | C→G | 8.2% | intergenic (+24/+4) | phrA → / ← yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| RA | BS168_reference_genome | 1,317,153:1 | +T | 100% | intergenic (+24/+4) | phrA → / ← yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| RA | BS168_reference_genome | 1,317,155 | T→C | 5.6% | intergenic (+26/+2) | phrA → / ← yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| RA | BS168_reference_genome | 1,349,495 | G→T | 70.8% | A325A (GCC→GCA) | pitB ← | putative low‑affinity inorganic phosphate transporter |
| RA | BS168_reference_genome | 1,463,035 | G→C | 5.6% | G153G (GGC→GGG) | ykwB ← | putative acetyltransferase / amidohydrolase |
| RA | BS168_reference_genome | 1,474,890 | C→T | 100% | L45L (TTG→TTA) | kre ← | regulator of transcription factor ComK function via modulation of mRNA stability |
| RA | BS168_reference_genome | 1,499,691 | G→T | 12.4% | intergenic (+26/‑198) | moaD → / → yknU | molybdopterin synthase (small subunit)/putative ABC transporter (ATP‑binding protein) |
| RA | BS168_reference_genome | 1,605,538 | T→A | 31.0% | intergenic (+48/‑92) | sigE → / → sigG | RNA polymerase sporulation‑specific sigma‑29 factor (sigma‑E)/RNA polymerase sporulation‑specific sigma factor (sigma‑G) |
| RA | BS168_reference_genome | 1,690,758 | C→A | 100% | R214S (CGT→AGT) | codY → | transcriptional regulator, GTP and BCAA‑dependent |
| RA | BS168_reference_genome | 1,749,907 | G→T | 31.1% | D164Y (GAC→TAC) | rnjB → | dual activity 5' exo‑and endoribonuclease J2 |
| RA | BS168_reference_genome | 1,994,711 | C→T | 35.4% | E1083K (GAA→AAA) | ppsA ← | non‑ribosomal plipastatin synthetase A involved in synthesis of plipastatin |
| RA | BS168_reference_genome | 2,097,080:1 | +A | 100% | intergenic (‑104/+46) | azoJ ← / ← yocK | FMN‑dependent NADH‑azoreductase/putative general stress protein |
| RA | BS168_reference_genome | 2,271,424 | T→C | 100% | R78R (AGA→AGG) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | BS168_reference_genome | 2,271,505 | C→T | 100% | V51V (GTG→GTA) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | BS168_reference_genome | 2,271,523 | A→C | 100% | D45E (GAT→GAG) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| JC | BS168_reference_genome | 2,344,013 | Δ39 bp | 71.0% | coding (2570‑2608/2745 nt) | ponA → | peptidoglycan glycosyltransferase (penicillin‑binding proteins 1A and 1B) |
| RA | BS168_reference_genome | 2,387,878:1 | +A | 100% | coding (711/735 nt) | yphF ← | putative lipoprotein of unknown function |
| RA | BS168_reference_genome | 2,480,646 | 2 bp→AT | 100% | 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 | 100% | 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 | 100% | intergenic (+42/+83) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | BS168_reference_genome | 2,553,074 | G→T | 6.8% | intergenic (+86/+7) | sinR → / ← tasA | master regulator of biofilm formation/major biofilm matrix component |
| RA | BS168_reference_genome | 2,581,726 | G→T | 5.4% | intergenic (‑109/+45) | pstS ← / ← pbpA | phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
| RA | BS168_reference_genome | 2,581,726:1 | +T | 100% | intergenic (‑109/+45) | pstS ← / ← pbpA | phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
| RA | BS168_reference_genome | 2,633,093 | C→T | 7.0% | G43E (GGG→GAG) | yqxA ← | conserved protein of unknown function |
| RA | BS168_reference_genome | 3,532,283 | C→G | 9.6% | P59P (CCC→CCG) | BSU_34399 → | hypothetical protein |
| RA | BS168_reference_genome | 3,532,310 | G→T | 5.4% | intergenic (+12/+15) | BSU_34399 → / ← padC | hypothetical protein/phenolic acid decarboxylase |
| RA | BS168_reference_genome | 3,764,135 | A→T | 20.1% | *258K (TAA→AAA) | mta ← | transcriptional regulator regulating efflux transporters synthesis (Fur‑independent bacillibactin export) |
| RA | BS168_reference_genome | 3,770,058:1 | +A | 100% | intergenic (‑250/+46) | ywzF ← / ← csbD | conserved protein of unknown function/stress response protein |
| RA | BS168_reference_genome | 3,807,717 | C→A | 11.4% | intergenic (‑342/+37) | murAB ← / ← tal | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase/transaldolase |
| RA | BS168_reference_genome | 3,807,763 | C→T | 14.5% | W210* (TGG→TGA) | tal ← | transaldolase |
| RA | BS168_reference_genome | 3,935,823 | Δ1 bp | 100% | intergenic (+35/+1) | ywbE → / ← rlmI | conserved protein of unknown function/large subunit ribosomal RNA m5C1962 methyltransferase |
| RA | BS168_reference_genome | 3,984,121 | G→T | 5.8% | intergenic (‑95/+12) | yxkH ← / ← msmX | putative exported polysaccharide deacetylase, lipoprotein/multiple sugar (maltodextrins) transporter ATP‑binding protein |
| RA | BS168_reference_genome | 4,153,115 | G→T | 100% | L192I (CTT→ATT) | walK ← | two‑component sensor histidine kinase [YycG] |
| RA | BS168_reference_genome | 4,155,390:1 | +A | 100% | intergenic (‑181/+43) | trnY‑Lys ← / ← purA | tRNA‑Lys/adenylosuccinate synthetase |
| RA | Exported | 1,922 | C→T | 27.3% | intergenic (–/‑1056) | – / → eryR | –//vntifkey=4 |
| JC | Exported | 2,210 | +TCTCG | 6.4% | intergenic (–/‑768) | – / → eryR | –//vntifkey=4 |
| RA | Exported | 2,224 | T→C | 6.4% | intergenic (–/‑754) | – / → eryR | –//vntifkey=4 |
| JC | Exported | 2,655 | Δ3 bp | 100% | intergenic (–/‑321) | – / → eryR | –//vntifkey=4 |
| JC | Exported | 3,843 | Δ5 bp | 100% | intergenic (+128/‑24) | eryR → / → ampR | /vntifkey=4//vntifkey=4 |
| RA | Exported | 5,049 | C→T | 100% | intergenic (+318/‑839) | ampR → / → lacZalpha | /vntifkey=4//vntifkey=4 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | BS168_reference_genome | 160931–164873 | 165633–164903 | 31–4703 | 176 [170] | [171] 173 | [rrnI‑16S]–[rrnI‑5S] | [rrnI‑16S],rrnI‑23S,[rrnI‑5S] |
| * | * | ÷ | BS168_reference_genome | 166405–166722 | 171286–170066 | 3345–4882 | 173 [171] | [171] 174 | rrnH‑16S–[rrnH‑5S] | rrnH‑16S,rrnH‑23S,[rrnH‑5S] |
| * | * | ÷ | BS168_reference_genome | 171415–171679 | 176264–172533 | 855–4850 | 172 [171] | [171] 172 | rrnG‑16S–[rrnG‑5S] | rrnG‑16S,rrnG‑23S,[rrnG‑5S] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | BS168_reference_genome | = 1073458 | 215 (0.730) | 101 (0.340) | 86/278 | NT | 29.8% | coding (260/612 nt) | scoC | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| ? | BS168_reference_genome | 1074991 = | 260 (0.880) | coding (174/519 nt) | trpP | tryptophan transporter or sensor | |||||
| * | ? | BS168_reference_genome | = 2152046 | 269 (0.910) | 13 (0.050) | 13/246 | NT | 5.4% | intergenic (+1/+40) | spsMn/sprB | spore capsular polysaccharide biosynthesis enzyme fragment; N‑terminal part of SpsM/recombination directionality factor; phage SPbeta |
| ? | BS168_reference_genome | 2286449 = | 222 (0.850) | pseudogene (2/606 nt) | spsMc | sporulation capsular polysaccharide biosynthesis enzyme C‑terminal end; restored upon phage SPbeta excision | |||||
| * | ? | BS168_reference_genome | 2653329 = | 240 (0.810) | 26 (0.090) | 24/268 | NT | 9.7% | pseudogene (337/471 nt) | sigKn | RNA polymerase sporulation‑specific sigma‑K factor precursor (Sigma‑27) (N‑terminal half) |
| ? | BS168_reference_genome | = 2701361 | 254 (0.890) | pseudogene (24/417 nt) | sigKc | RNA polymerase sporulation‑specific sigma‑K factor precursor (Sigma‑27) (C‑terminal fragment) | |||||
| * | ? | BS168_reference_genome | = 2653333 | 242 (0.820) | 25 (0.090) | 22/268 | NT | 9.3% | pseudogene (341/471 nt) | sigKn | RNA polymerase sporulation‑specific sigma‑K factor precursor (Sigma‑27) (N‑terminal half) |
| ? | BS168_reference_genome | 2701367 = | 254 (0.890) | pseudogene (30/417 nt) | sigKc | RNA polymerase sporulation‑specific sigma‑K factor precursor (Sigma‑27) (C‑terminal fragment) | |||||
| * | ? | Exported | = 1838 | 15158 (0.700) | 3944 (0.180) | 251/274 | NT | 23.8% | intergenic (–/‑1140) | –/eryR | –//vntifkey=4 |
| ? | Exported | 2572 = | 10290 (0.480) | intergenic (–/‑406) | –/eryR | –//vntifkey=4 | |||||