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 | 78,236 | A→T | 26.6% | N418I (AAT→ATT) | ftsH → | ATP‑dependent cytoplasmic membrane protease |
| 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 | 333,932 | G→A | 15.2% | L16L (CTC→CTT) | mdr ← | multidrug‑efflux transporter |
| 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 | 474,638 | G→T | 5.7% | intergenic (+413/‑93) | ydaG → / → amj | putative general stress protein/lipid II flippase |
| JC | BS168_reference_genome | 490,580 | +TTT | 15.4% | coding (170/204 nt) | BSU_04345 ← | hypothetical protein |
| RA | BS168_reference_genome | 506,071 | C→A | 20.9% | 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 | 608,214:1 | +A | 100% | intergenic (‑139/+32) | ydgF ← / ← dinB | putative amino acid permease/nuclease inhibitor |
| RA | BS168_reference_genome | 696,015 | G→T | 12.4% | intergenic (+31/‑180) | pbuG → / → yebC | hypoxanthine/guanine permease/putative integral inner membrane protein |
| RA | BS168_reference_genome | 771,300 | C→T | 25.1% | A356V (GCG→GTG) | rhgW → | rhamnogalacturonan endolyase |
| RA | BS168_reference_genome | 892,022 | A→T | 100% | N196I (AAT→ATT) | malR → | transcriptional activator of the Mal operon |
| RA | BS168_reference_genome | 961,062 | Δ1 bp | 37.5% | intergenic (‑76/‑332) | katA ← / → ssuB | vegetative catalase 1/aliphatic sulfonate ABC transporter (ATP‑binding protein) |
| RA | BS168_reference_genome | 961,069 | G→T | 36.2% | intergenic (‑83/‑325) | katA ← / → ssuB | vegetative catalase 1/aliphatic sulfonate ABC transporter (ATP‑binding protein) |
| RA | BS168_reference_genome | 1,073,374 | C→T | 14.4% | W115* (TGG→TAG) | scoC ← | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| RA | BS168_reference_genome | 1,073,401 | A→T | 22.2% | L106* (TTG→TAG) | scoC ← | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| RA | BS168_reference_genome | 1,073,672 | A→T | 26.4% | F16I (TTC→ATC) | scoC ← | transcriptional regulator of extracellular protease production, sporulation and bacilysin production (MarR family) |
| RA | BS168_reference_genome | 1,080,047 | C→T | 5.9% | A209V (GCC→GTC) | ecsC → | putative hydrolase |
| RA | BS168_reference_genome | 1,140,541 | A→G | 6.0% | K245K (AAA→AAG) | addA → | ATP‑dependent deoxyribonuclease (subunit A) |
| RA | BS168_reference_genome | 1,224,521 | A→G | 38.0% | E356G (GAA→GGA) | oppD → | oligopeptide ABC transporter (ATP‑binding protein) |
| RA | BS168_reference_genome | 1,248,775 | A→T | 21.8% | K37N (AAA→AAT) | cotO → | spore outer coat protein |
| 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 | 91.1% | 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 | 7.0% | 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 | 1,323,881 | C→T | 30.5% | P27L (CCG→CTG) | xkdD → | phage PBSX; conserved hypothetical protein |
| 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 | 30.9% | intergenic (+30/‑66) | ykzU → / → ykuH | conserved hypothetical protein/conserved protein of unknown function |
| RA | BS168_reference_genome | 1,524,173 | T→G | 24.1% | T205P (ACC→CCC) | rnjA ← | ribonuclease J1 |
| RA | BS168_reference_genome | 1,544,043 | C→T | 18.4% | F76F (TTC→TTT) | ylaB → | hypothetical protein |
| RA | BS168_reference_genome | 1,690,758 | C→G | 44.2% | R214G (CGT→GGT) ‡ | codY → | transcriptional regulator, GTP and BCAA‑dependent |
| RA | BS168_reference_genome | 1,690,759 | G→A | 53.7% | R214H (CGT→CAT) ‡ | codY → | transcriptional regulator, GTP and BCAA‑dependent |
| RA | BS168_reference_genome | 2,063,773 | T→A | 28.7% | pseudogene (391/654 nt) | yobHc ← | fragment of putative DNA phage repair protein; putative defective prophage 6 |
| 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 | 2,291,897 | C→A | 25.1% | 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 | 2,480,646 | 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 | 2,805,209 | G→A | 15.4% | G185S (GGC→AGC) | glnP → | glutamine ABC transporter (permease) |
| RA | BS168_reference_genome | 2,989,790 | C→A | 11.7% | intergenic (‑225/+110) | accD ← / ← maeB | acetyl‑CoA carboxylase (carboxyltransferase beta subunit)/NADP‑dependent malic enzyme (conversion of malate into pyruvate, anabolic) |
| RA | BS168_reference_genome | 2,989,829 | G→C | 10.8% | intergenic (‑264/+71) | accD ← / ← maeB | acetyl‑CoA carboxylase (carboxyltransferase beta subunit)/NADP‑dependent malic enzyme (conversion of malate into pyruvate, anabolic) |
| RA | BS168_reference_genome | 2,992,352 | C→T | 22.5% | L755L (TTG→TTA) | dnaEC ← | DNA polymerase III (alpha subunit), DnaE3 |
| RA | BS168_reference_genome | 3,056,838 | G→T | 11.9% | intergenic (+42/+11) | ytzB → / ← maeC | conserved protein of unknown function/NAD‑dependent malic enzyme (conversion of malate into pyruvate) |
| RA | BS168_reference_genome | 3,139,266 | T→C | 26.3% | intergenic (‑40/‑165) | rpmEB ← / → ythA | ribosomal protein L31/putative cytochrome bd menaquinol oxidase subunit I |
| RA | BS168_reference_genome | 3,373,796 | T→A | 16.8% | D18E (GAT→GAA) | yuzM → | conserved protein of unknown function |
| RA | BS168_reference_genome | 3,532,310 | G→T | 7.9% | intergenic (+12/+15) | BSU_34399 → / ← padC | hypothetical protein/phenolic acid decarboxylase |
| RA | BS168_reference_genome | 3,532,311 | G→T | 10.0% | intergenic (+13/+14) | BSU_34399 → / ← padC | hypothetical protein/phenolic acid decarboxylase |
| RA | BS168_reference_genome | 3,764,135 | A→T | 20.8% | *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 | 3,935,823 | 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 | 8.2% | 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 |
| JC | pSIJ663_pHT315_araE_xy | 2,210 | +TCTCG | 7.8% | intergenic (–/‑768) | – / → eryR | –/– |
| JC | pSIJ663_pHT315_araE_xy | 2,655 | Δ3 bp | 100% | intergenic (–/‑321) | – / → eryR | –/– |
| JC | pSIJ663_pHT315_araE_xy | 3,843 | Δ5 bp | 100% | intergenic (+128/‑24) | eryR → / → ampR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 5,049 | C→T | 100% | intergenic (+318/–) | ampR → / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | BS168_reference_genome | 166412–166797 | 171238–170066 | 3270–4827 | 179 [175] | [175] 179 | rrnH‑16S–[rrnH‑5S] | rrnH‑16S,rrnH‑23S,[rrnH‑5S] |
| * | * | ÷ | BS168_reference_genome | 171449–171679 | 176256–172533 | 855–4808 | 180 [177] | [177] 179 | rrnG‑16S–[rrnG‑5S] | rrnG‑16S,rrnG‑23S,[rrnG‑5S] |
| * | * | ÷ | BS168_reference_genome | 3485230–3485468 | 3486758 | 1291–1529 | 179 [176] | [1] 330 | [araE]–[araR] | [araE],[araR] |
| * | * | ÷ | pSIJ663_pHT315_araE_xy | 5552 | 11186–9803 | 4252–5635 | 43114 [46] | [34866] 35100 | ampR/– | –/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | BS168_reference_genome | 3484072 = | NA (NA) | 2105 (0.140) | 13/272 | NT | 5.2% | coding (1395/1395 nt) | araE | arabinose‑related compounds permease |
| ? | pSIJ663_pHT315_araE_xy | = 11232 | 39518 (1.280) | intergenic (+6501/–) | ampR/– | –/– | |||||
| * | ? | BS168_reference_genome | 3486759 = | 1 (0.000) | 203 (0.020) +50 bp |
116/178 | NT | 99.8% | intergenic (+1/+48) | araR/yvbT | transcriptional repressor of the ara regulon (LacI family)/putative alkanal monooxygenase |
| ? | pSIJ663_pHT315_araE_xy | 9781 = | 0 (0.000) | intergenic (+5050/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5551 | 18 (0.000) | 38394 (1.300) | 268/268 | NT | 100.0% | intergenic (+820/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9889 = | NA (NA) | intergenic (+5158/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5614 | 0 (0.000) | 34 (0.000) | 32/272 | NT | 100% | intergenic (+883/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9532 = | 0 (0.000) | intergenic (+4801/–) | ampR/– | –/– | |||||