mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 20,055 | G→C | 8.7% | V30L (GTA→CTA) | pdxT → | glutamine amidotransferase for pyridoxal phosphate synthesis; pyridoxal 5'‑phosphate synthase complex, glutamine amidotransferase subunit PdxT |
| RA | BS168_reference_genome | 113,389 | A→G | 7.7% | E197G (GAA→GGA) | cysE → | serine O‑acetyltransferase |
| 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 | 380,714 | G→A | 7.3% | P1249P (CCG→CCA) | srfAA → | surfactin synthetase |
| RA | BS168_reference_genome | 442,499 | C→T | 10.8% | T310M (ACG→ATG) | gabT → | 4‑aminobutyrate aminotransferase |
| RA | BS168_reference_genome | 557,865:1 | +T | 100% | intergenic (+416/‑8) | yddT → / → ydzN | putative exported phage protein/hypothetical protein |
| RA | BS168_reference_genome | 592,831 | G→T | 5.5% | H125Q (CAC→CAA) | cesA ← | carboxylesterase NP |
| RA | BS168_reference_genome | 727,505 | C→G | 10.3% | G272R (GGC→CGC) | opuE ← | proline transporter |
| RA | BS168_reference_genome | 892,022 | A→T | 100% | N196I (AAT→ATT) | malR → | transcriptional activator of the Mal operon |
| RA | BS168_reference_genome | 934,016 | C→T | 13.8% | T713I (ACC→ATC) | yfhO → | conserved membrane protein |
| RA | BS168_reference_genome | 961,032:1 | +A | 100% | intergenic (‑46/‑362) | katA ← / → ssuB | vegetative catalase 1/aliphatic sulfonate ABC transporter (ATP‑binding protein) |
| RA | BS168_reference_genome | 996,888 | G→T | 13.8% | K82N (AAG→AAT) | yhcU → | conserved protein of unknown function |
| RA | BS168_reference_genome | 1,006,868 | A→C | 12.5% | Q32P (CAG→CCG) | pgcA → | alpha‑phosphoglucomutase |
| RA | BS168_reference_genome | 1,044,003 | T→C | 7.8% | I82V (ATC→GTC) | nhaC ← | Na+/H+ antiporter |
| RA | BS168_reference_genome | 1,073,040 | C→T | 100% | A91A (GCC→GCT) | yhaI → | conserved protein of unknown function |
| RA | BS168_reference_genome | 1,073,489 | C→T | 100% | A77T (GCA→ACA) | scoC ← | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| RA | BS168_reference_genome | 1,074,835 | C→T | 100% | G110G (GGG→GGA) | trpP ← | tryptophan transporter or sensor |
| RA | BS168_reference_genome | 1,159,412 | A→G | 5.3% | H93H (CAT→CAC) | yizA ← | conserved hypothetical protein (sporulation related) |
| RA | BS168_reference_genome | 1,213,393 | C→T | 8.7% | P312S (CCA→TCA) | appF → | oligopeptide ABC transporter (ATP‑binding protein) |
| RA | BS168_reference_genome | 1,241,555 | G→T | 16.7% | E400D (GAG→GAT) | kefQ → | gated K+/H+ antiporter |
| RA | BS168_reference_genome | 1,253,605 | T→C | 8.1% | F74S (TTT→TCT) | spoVIF → | sporulation‑specific protein needed for heat resistance |
| RA | BS168_reference_genome | 1,255,382 | T→C | 7.0% | Y204C (TAC→TGC) | yjcD ← | putative ATP‑dependent DNA helicase (sporulation associated) |
| RA | BS168_reference_genome | 1,317,152:1 | +GT | 100% | intergenic (+23/+5) | 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 | 1,364,966 | T→C | 10.0% | F272F (TTT→TTC) | dppE → | dipeptide ABC transporter (dipeptide‑binding lipoprotein) |
| RA | BS168_reference_genome | 1,473,747 | T→C | 11.1% | V48A (GTG→GCG) | cheV → | coupling protein and response regulator for CheA activity in response to attractants (chemotaxis) |
| 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 | 1,494,589 | T→C | 9.3% | E260E (GAA→GAG) | sppO ← | spore protein cse15 |
| RA | BS168_reference_genome | 1,690,758 | C→A | 100% | R214S (CGT→AGT) | codY → | transcriptional regulator, GTP and BCAA‑dependent |
| RA | BS168_reference_genome | 1,742,383 | G→A | 8.9% | D256N (GAT→AAT) | ylxY → | putative sugar deacetylase |
| RA | BS168_reference_genome | 1,904,636 | T→A | 8.5% | V38V (GTA→GTT) | ynzK ← | putative membrane protein of unknown function (phage origin) |
| RA | BS168_reference_genome | 1,910,707 | C→T | 20.0% | P181S (CCG→TCG) | yndF → | putative spore germination lipoprotein |
| RA | BS168_reference_genome | 1,910,754 | C→T | 19.9% | S196S (TCC→TCT) | yndF → | putative spore germination lipoprotein |
| 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 |
| RA | BS168_reference_genome | 2,387,878:1 | +A | 100% | coding (711/735 nt) | yphF ← | putative lipoprotein of unknown function |
| RA | BS168_reference_genome | 2,403,857 | C→G | 33.6% | K78N (AAG→AAC) | mecB ← | adaptor to ClpC; regulator of competence and sporulation |
| RA | BS168_reference_genome | 2,412,532 | G→T | 7.4% | V483F (GTT→TTT) | serA → | 3‑phosphoglycerate dehydrogenase |
| 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 | 2,581,726:1 | +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 | 100% | G43E (GGG→GAG) | yqxA ← | conserved protein of unknown function |
| RA | BS168_reference_genome | 2,770,869 | C→T | 100% | R174C (CGT→TGT) | rsiV → | anti‑sigma(V) factor |
| RA | BS168_reference_genome | 2,831,221 | A→G | 12.9% | L187S (TTG→TCG) | yrbG ← | conserved hypothetical protein |
| RA | BS168_reference_genome | 2,842,959 | A→G | 6.8% | Q450R (CAA→CGA) | alaP → | sodium/proton‑dependent alanine transporter |
| RA | BS168_reference_genome | 2,861,703 | C→T | 15.3% | A16T (GCG→ACG) | mreB ← | cell‑shape determining protein |
| RA | BS168_reference_genome | 2,907,559 | C→A | 10.5% | L179L (CTG→CTT) | sdhA ← | succinate dehydrogenase (flavoprotein subunit) |
| RA | BS168_reference_genome | 3,104,817 | A→G | 12.1% | M76T (ATG→ACG) | leuS ← | leucyl‑tRNA synthetase |
| RA | BS168_reference_genome | 3,136,949 | G→A | 6.8% | H143Y (CAT→TAT) | ytkA ← | putative lipoprotein |
| RA | BS168_reference_genome | 3,287,650 | A→G | 9.7% | P2P (CCT→CCC) | dhbF ← | siderophore 2,3‑dihydroxybenzoate‑glycine‑threonine trimeric ester bacillibactin synthetase |
| RA | BS168_reference_genome | 3,376,306 | A→G | 11.1% | M451V (ATG→GTG) | mdtP → | multidrug‑efflux transporter |
| RA | BS168_reference_genome | 3,471,869 | T→C | 12.5% | K203R (AAA→AGA) | yvbG ← | putative integral membrane protein |
| RA | BS168_reference_genome | 3,503,708 | A→G | 8.3% | V459A (GTC→GCC) | ganA ← | short chain beta‑1,4‑galacto‑oligosaccharides beta‑galactosidase (beta‑galacto‑pyranoside hydrolase) |
| 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 | 3,935,823 | Δ1 bp | 100% | intergenic (+35/+1) | ywbE → / ← rlmI | conserved protein of unknown function/large subunit ribosomal RNA m5C1962 methyltransferase |
| RA | BS168_reference_genome | 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 | BS168_reference_genome | 4,174,602 | A→T | 5.7% | S65C (AGT→TGT) | yybL → | putative transporter permease subunit |
| RA | BS168_reference_genome | 4,191,127 | A→G | 10.8% | intergenic (+1/‑71) | yyaM → / → yyaL | putative efflux transporter/conserved hypothetical protein |
| RA | Exported | 121 | G→C | 5.4% | intergenic (–/‑2857) | – / → eryR | –//vntifkey=4 |
| RA | Exported | 131 | G→C | 6.9% | intergenic (–/‑2847) | – / → eryR | –//vntifkey=4 |
| RA | Exported | 2,039 | C→T | 18.6% | intergenic (–/‑939) | – / → eryR | –//vntifkey=4 |
| RA | Exported | 2,205 | C→T | 8.0% | intergenic (–/‑773) | – / → eryR | –//vntifkey=4 |
| RA | Exported | 2,206 | C→T | 8.0% | intergenic (–/‑772) | – / → eryR | –//vntifkey=4 |
| JC | Exported | 2,210 | +TCTCG | 12.5% | intergenic (–/‑768) | – / → eryR | –//vntifkey=4 |
| RA | Exported | 2,214 | C→T | 11.0% | intergenic (–/‑764) | – / → eryR | –//vntifkey=4 |
| JC | Exported | 2,655 | Δ3 bp | 100% | intergenic (–/‑321) | – / → eryR | –//vntifkey=4 |
| RA | Exported | 3,729 | T→G | 6.8% | intergenic (+14/‑142) | eryR → / → ampR | /vntifkey=4//vntifkey=4 |
| RA | Exported | 3,735 | A→T | 9.3% | intergenic (+20/‑136) | eryR → / → ampR | /vntifkey=4//vntifkey=4 |
| RA | Exported | 3,741 | G→T | 9.8% | intergenic (+26/‑130) | eryR → / → ampR | /vntifkey=4//vntifkey=4 |
| RA | Exported | 3,783 | G→T | 5.1% | intergenic (+68/‑88) | eryR → / → ampR | /vntifkey=4//vntifkey=4 |
| JC | Exported | 3,843 | Δ5 bp | 100% | intergenic (+128/‑24) | eryR → / → ampR | /vntifkey=4//vntifkey=4 |
| RA | Exported | 4,625 | A→C | 6.6% | K252T (AAG→ACG) | ampR → | /vntifkey=4 |
| RA | Exported | 4,648 | T→A | 11.3% | Y260N (TAC→AAC) ‡ | ampR → | /vntifkey=4 |
| RA | Exported | 4,649 | A→C | 9.3% | Y260S (TAC→TCC) ‡ | ampR → | /vntifkey=4 |
| RA | Exported | 5,049 | C→T | 100% | intergenic (+318/‑839) | ampR → / → lacZalpha | /vntifkey=4//vntifkey=4 |
| RA | Exported | 5,173 | T→G | 6.5% | intergenic (+442/‑715) | ampR → / → lacZalpha | /vntifkey=4//vntifkey=4 |
| RA | Exported | 5,302 | A→C | 5.4% | intergenic (+571/‑586) | ampR → / → lacZalpha | /vntifkey=4//vntifkey=4 |
| RA | Exported | 5,464 | T→G | 5.4% | intergenic (+733/‑424) | ampR → / → lacZalpha | /vntifkey=4//vntifkey=4 |
| RA | Exported | 6,006 | T→G | 6.1% | V40G (GTT→GGT) | lacZalpha → | /vntifkey=4 |
| RA | Exported | 6,012 | A→C | 7.3% | Q42P (CAA→CCA) | lacZalpha → | /vntifkey=4 |
| RA | Exported | 6,031 | A→C | 6.4% | A48A (GCA→GCC) | lacZalpha → | /vntifkey=4 |
| RA | Exported | 6,033 | A→C | 5.0% | H49P (CAT→CCT) | lacZalpha → | /vntifkey=4 |
| RA | Exported | 6,256 | A→C | 5.4% | intergenic (+45/–) | lacZalpha → / – | /vntifkey=4/– |
| RA | Exported | 6,277 | A→C | 5.3% | intergenic (+66/–) | lacZalpha → / – | /vntifkey=4/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | BS168_reference_genome | 160976–161238 | 165590–164903 | 3666–4615 | 5 [4] | [2] 5 | [rrnI‑16S]–rrnI‑23S | [rrnI‑16S],rrnI‑23S |
| * | * | ÷ | BS168_reference_genome | 166450–166702 | 171216–170393 | 3692–4767 | 5 [4] | [3] 5 | rrnH‑16S–[rrnH‑5S] | rrnH‑16S,rrnH‑23S,[rrnH‑5S] |
| * | * | ÷ | BS168_reference_genome | 171474–171678 | 176227–172977 | 1300–4754 | 5 [4] | [3] 6 | rrnG‑16S–[rrnG‑5S] | rrnG‑16S,rrnG‑23S,[rrnG‑5S] |
| * | * | ÷ | BS168_reference_genome | 616339 | 616412 | 74 | 5 [3] | [4] 5 | ydhC | putative transcriptional regulator (GntR family) |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | BS168_reference_genome | 2653329 = | 22 (0.700) | 5 (0.170) | 5/224 | NT | 26.3% | pseudogene (337/471 nt) | sigKn | RNA polymerase sporulation‑specific sigma‑K factor precursor (Sigma‑27) (N‑terminal half) |
| ? | BS168_reference_genome | = 2701361 | 7 (0.230) | pseudogene (24/417 nt) | sigKc | RNA polymerase sporulation‑specific sigma‑K factor precursor (Sigma‑27) (C‑terminal fragment) | |||||
| * | ? | BS168_reference_genome | = 2653333 | 22 (0.700) | 3 (0.100) | 3/224 | NT | 17.6% | pseudogene (341/471 nt) | sigKn | RNA polymerase sporulation‑specific sigma‑K factor precursor (Sigma‑27) (N‑terminal half) |
| ? | BS168_reference_genome | 2701367 = | 7 (0.230) | pseudogene (30/417 nt) | sigKc | RNA polymerase sporulation‑specific sigma‑K factor precursor (Sigma‑27) (C‑terminal fragment) | |||||
| * | ? | Exported | = 1838 | 78 (0.000) | 28746 (1.490) | 225/230 | NT | 99.8% | intergenic (–/‑1140) | –/eryR | –//vntifkey=4 |
| ? | Exported | 2572 = | 25 (0.000) | intergenic (–/‑406) | –/eryR | –//vntifkey=4 | |||||