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 | 86,766 | T→C | 9.1% | C60C (TGT→TGC) | folB → | dihydroneopterin aldolase |
| RA | BS168_reference_genome | 88,548 | C→T | 11.7% | C305C (TGC→TGT) | dusB → | tRNA‑dihydrouridine synthase B |
| RA | BS168_reference_genome | 96,240 | G→A | 7.3% | intergenic (+19/‑152) | trnJ‑Ala → / → rrnW‑16S | tRNA‑Ala/ribosomal RNA‑16S |
| 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 | 498,343 | G→A | 12.9% | L192L (CTG→CTA) | dctS → | two‑component sensor histidine kinase |
| RA | BS168_reference_genome | 506,071 | C→A | 88.4% | P307Q (CCG→CAG) | ydbM → | putative acyl‑CoA dehydrogenase |
| RA | BS168_reference_genome | 557,865:1 | +T | 100% | intergenic (+416/‑8) | yddT → / → ydzN | putative exported phage protein/hypothetical protein |
| RA | BS168_reference_genome | 675,819 | C→T | 11.4% | L13L (TTG→TTA) | ydjJ ← | putative membrane associated potassium channel; prophage region 3 |
| RA | BS168_reference_genome | 693,081 | C→T | 12.1% | I114I (ATC→ATT) | guaA → | GMP synthetase |
| RA | BS168_reference_genome | 892,022 | A→T | 100% | N196I (AAT→ATT) | malR → | transcriptional activator of the Mal operon |
| 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 | 966,786 | G→A | 7.3% | T29I (ACT→ATT) | ygzD ← | putative HTH‑type transcriptional regulator |
| RA | BS168_reference_genome | 966,850 | G→T | 6.3% | L8M (CTG→ATG) | ygzD ← | putative HTH‑type transcriptional regulator |
| RA | BS168_reference_genome | 1,023,150 | C→A | 20.8% | intergenic (+50/‑200) | yhdF → / → bcaP | putative NAD(P)‑dependent dehydrogenase/branched‑chain amino acid transporter or methylthioribose‑degradation metabolite exporter |
| RA | BS168_reference_genome | 1,023,198 | G→T | 19.2% | intergenic (+98/‑152) | yhdF → / → bcaP | putative NAD(P)‑dependent dehydrogenase/branched‑chain amino acid transporter or methylthioribose‑degradation metabolite exporter |
| RA | BS168_reference_genome | 1,069,077 | A→T | 9.1% | E12D (GAA→GAT) | yhaM → | 3'‑5' exonuclease |
| RA | BS168_reference_genome | 1,073,672 | A→T | 100% | F16I (TTC→ATC) | scoC ← | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| RA | BS168_reference_genome | 1,116,820 | G→C | 8.7% | intergenic (‑4/‑289) | yhzC ← / → comK | conserved protein of unknown function/competence transcription factor (CTF) |
| RA | BS168_reference_genome | 1,249,964 | A→T | 11.5% | intergenic (‑76/+52) | cotZ ← / ← cotY | spore coat protein (insoluble fraction, crust layer)/outer spore coat protein (crust layer, insoluble fraction) |
| 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 | 1,459,888 | T→C | 10.0% | L80P (CTC→CCC) | ptsI → | phosphotransferase system (PTS) enzyme I |
| 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 | 1,481,481 | T→C | 100% | intergenic (+30/‑66) | ykzU → / → ykuH | conserved hypothetical protein/conserved protein of unknown function |
| RA | BS168_reference_genome | 1,524,173 | T→G | 100% | T205P (ACC→CCC) | rnjA ← | ribonuclease J1 |
| RA | BS168_reference_genome | 1,555,230 | T→C | 11.7% | V349A (GTT→GCT) | pycA → | pyruvate carboxylase |
| RA | BS168_reference_genome | 1,593,713 | G→A | 14.2% | G4S (GGT→AGT) | divIB → | cell‑division initiation protein |
| RA | BS168_reference_genome | 1,690,759 | G→A | 100% | R214H (CGT→CAT) | codY → | transcriptional regulator, GTP and BCAA‑dependent |
| RA | BS168_reference_genome | 1,780,750 | Δ1 bp | 7.0% | coding (324/456 nt) | ymzD ← | putative integral inner membrane protein |
| RA | BS168_reference_genome | 1,807,419 | A→T | 9.0% | I4872F (ATC→TTC) | pksJ → | polyketide synthase of type I involved in nonribosomal synthesis of bacillaene |
| RA | BS168_reference_genome | 1,815,227 | T→C | 9.3% | V2436A (GTT→GCT) | pksL → | polyketide synthase of type I (bacillaene synthesis) |
| RA | BS168_reference_genome | 1,904,668 | T→C | 11.1% | T28A (ACA→GCA) | ynzK ← | putative membrane protein of unknown function (phage origin) |
| RA | BS168_reference_genome | 1,924,696 | T→G | 18.2% | F76V (TTT→GTT) | yneJ → | putative integral inner membrane protein |
| RA | BS168_reference_genome | 2,022,177 | T→C | 6.8% | E97E (GAA→GAG) | yoaB ← | negatively charged metabolite transporter |
| RA | BS168_reference_genome | 2,089,139 | G→T | 8.0% | G295* (GGA→TGA) | yocD → | putative carboxypeptidase; aminoacid adenylate hydrolase (microcin resistance) |
| 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 | 2,153,853 | T→C | 12.1% | E76E (GAA→GAG) | yotI ← | conserved hypothetical protein; phage SPbeta |
| 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 | 2,291,897 | C→A | 93.0% | E130* (GAG→TAG) | scuA ← | assembly factor BSco of the Cu(A) site of cytochrome c oxidase |
| RA | BS168_reference_genome | 2,387,878:1 | +A | 100% | coding (711/735 nt) | yphF ← | putative lipoprotein of unknown function |
| RA | BS168_reference_genome | 2,401,489 | T→A | 11.5% | D157V (GAT→GTT) | ypdA ← | putative bacillithiol biosynthesis thiol disulfide oxidoreductase |
| 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 | 2,581,941 | A→G | 11.4% | W661R (TGG→CGG) | pbpA ← | transpeptidase (penicillin‑binding protein 2A) |
| RA | BS168_reference_genome | 2,726,114 | G→A | 8.9% | R93H (CGT→CAT) | gltR → | transcriptional regulator (LysR family) |
| RA | BS168_reference_genome | 2,738,963 | A→T | 12.5% | D219V (GAT→GTT) | murI → | glutamate racemase |
| RA | BS168_reference_genome | 2,753,394 | T→A | 5.9% | N110K (AAT→AAA) | yraF → | putative spore coat protein |
| RA | BS168_reference_genome | 2,794,537 | A→T | 13.8% | Y180* (TAT→TAA) | yrrN ← | putative hydrolase small subunit |
| RA | BS168_reference_genome | 2,844,699 | G→A | 11.2% | G380G (GGC→GGT) | safA ← | morphogenetic protein associated with SpoVID |
| RA | BS168_reference_genome | 2,992,352 | C→T | 100% | L755L (TTG→TTA) | dnaEC ← | DNA polymerase III (alpha subunit), DnaE3 |
| RA | BS168_reference_genome | 3,255,603 | T→C | 7.9% | H79R (CAT→CGT) | comP ← | two‑component sensor histidine kinase |
| RA | BS168_reference_genome | 3,425,067 | A→G | 8.9% | L32P (CTG→CCG) | yvgK ← | putative molybdate binding regulator |
| RA | BS168_reference_genome | 3,483,689 | A→G | 12.5% | I29T (ATC→ACC) | cggR ← | transcriptional regulator of gapA |
| RA | BS168_reference_genome | 3,501,653 | A→G | 9.9% | *430R (TGA→CGA) | ganB ← | endo‑beta‑1,4‑galactanase |
| RA | BS168_reference_genome | 3,613,675 | T→G | 16.0% | D419A (GAC→GCC) | uvrB ← | excinuclease ABC (subunit B) |
| RA | BS168_reference_genome | 3,621,914 | T→C | 6.7% | pseudogene (43/339 nt) | swrAAc ← | swarming motility protein fragment; C‑terminal part of swrAA |
| 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 | 3,811,194 | G→T | 10.0% | Y369* (TAC→TAA) | pyrG ← | CTP synthetase |
| 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 | 3,947,046 | G→A | 10.4% | intergenic (+137/‑112) | tyrZR → / → tyrZ | transcriptional regulator controlling expression of tyrZ/tyrosyl‑tRNA synthetase |
| RA | BS168_reference_genome | 3,963,785 | G→T | 11.1% | S48R (AGC→AGA) | licR ← | transcriptional activator of the lichenan operon |
| RA | BS168_reference_genome | 3,970,004 | C→T | 12.9% | G106R (GGA→AGA) | yxlC ← | sigma‑Y antisigma factor |
| RA | BS168_reference_genome | 3,994,995 | T→G | 22.4% | V209V (GTT→GTG) | yxjL → | two‑component response regulator [YxjM] |
| RA | BS168_reference_genome | 4,140,276 | C→A | 10.5% | P6H (CCC→CAC) | rapG → | response regulator aspartate phosphatase |
| RA | BS168_reference_genome | 4,150,153 | A→G | 8.1% | D119D (GAT→GAC) | walI ← | regulator of WalRK |
| 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 | 4,177,166 | A→G | 7.1% | Y175H (TAC→CAC) | ictI ← | inner spore coat protein |
| RA | pSIJ663_pHT315_araE_xy | 78 | G→T | 5.1% | intergenic (–/‑2900) | – / → eryR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 116 | T→A | 5.1% | intergenic (–/‑2862) | – / → eryR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 131 | G→C | 7.3% | intergenic (–/‑2847) | – / → eryR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 137 | A→C | 5.8% | intergenic (–/‑2841) | – / → eryR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 1,963 | C→T | 5.1% | intergenic (–/‑1015) | – / → eryR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 2,207 | C→T | 8.3% | intergenic (–/‑771) | – / → eryR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 2,231 | A→G | 15.9% | intergenic (–/‑747) | – / → eryR | –/– |
| JC | pSIJ663_pHT315_araE_xy | 2,655 | Δ3 bp | 100% | intergenic (–/‑321) | – / → eryR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 3,729 | T→G | 7.2% | intergenic (+14/‑142) | eryR → / → ampR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 3,735 | A→T | 10.0% | intergenic (+20/‑136) | eryR → / → ampR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 3,741 | G→T | 10.0% | intergenic (+26/‑130) | eryR → / → ampR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 3,743 | A→T | 6.0% | intergenic (+28/‑128) | eryR → / → ampR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 3,749 | A→T | 5.7% | intergenic (+34/‑122) | eryR → / → ampR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 3,783 | G→T | 5.4% | intergenic (+68/‑88) | eryR → / → ampR | –/– |
| JC | pSIJ663_pHT315_araE_xy | 3,843 | Δ5 bp | 100% | intergenic (+128/‑24) | eryR → / → ampR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 4,625 | A→C | 7.1% | K252T (AAG→ACG) | ampR → | |
| RA | pSIJ663_pHT315_araE_xy | 4,648 | T→A | 11.1% | Y260N (TAC→AAC) ‡ | ampR → | |
| RA | pSIJ663_pHT315_araE_xy | 4,649 | A→C | 9.3% | Y260S (TAC→TCC) ‡ | ampR → | |
| RA | pSIJ663_pHT315_araE_xy | 5,049 | C→T | 100% | intergenic (+318/–) | ampR → / – | –/– |
| RA | pSIJ663_pHT315_araE_xy | 5,173 | T→G | 6.4% | intergenic (+442/–) | ampR → / – | –/– |
| RA | pSIJ663_pHT315_araE_xy | 5,302 | A→C | 6.1% | intergenic (+571/–) | ampR → / – | –/– |
| RA | pSIJ663_pHT315_araE_xy | 5,464 | T→G | 6.0% | intergenic (+733/–) | ampR → / – | –/– |
| RA | pSIJ663_pHT315_araE_xy | 5,467 | T→G | 5.6% | intergenic (+736/–) | ampR → / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | BS168_reference_genome | 160964–161238 | 165598–164903 | 3666–4635 | 9 [6] | [5] 9 | [rrnI‑16S]–[rrnI‑5S] | [rrnI‑16S],rrnI‑23S,[rrnI‑5S] |
| * | * | ÷ | BS168_reference_genome | 166445–166702 | 171225–170391 | 3690–4781 | 7 [6] | [6] 7 | rrnH‑16S–[rrnH‑5S] | rrnH‑16S,rrnH‑23S,[rrnH‑5S] |
| * | * | ÷ | BS168_reference_genome | 171475–171676 | 176238–174753 | 3078–4764 | 7 [4] | [5] 12 | rrnG‑16S–[rrnG‑5S] | rrnG‑16S,rrnG‑23S,[rrnG‑5S] |
| * | * | ÷ | BS168_reference_genome | 3485351–3485451 | 3486758 | 1308–1408 | 10 [6] | [0] 34 | [araE]–[araR] | [araE],[araR] |
| * | * | ÷ | pSIJ663_pHT315_araE_xy | 5552 | 11154–9820 | 4269–5603 | 5817 [43] | [3245] 3736 | ampR/– | –/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | BS168_reference_genome | 3486759 = | 0 (0.000) | 17 (0.010) +50 bp |
14/130 | NT | 92.3% | intergenic (+1/+48) | araR/yvbT | transcriptional repressor of the ara regulon (LacI family)/putative alkanal monooxygenase |
| ? | pSIJ663_pHT315_araE_xy | 9781 = | 5 (0.000) | intergenic (+5050/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5551 | 12 (0.000) | 5055 (1.120) | 190/220 | NT | 99.8% | intergenic (+820/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9889 = | NA (NA) | intergenic (+5158/–) | ampR/– | –/– | |||||