breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | ||||||
---|---|---|---|---|---|---|
evidence | position | mutation | freq | annotation | gene | description |
RA | 161,068 | A→C | 24.0% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
RA | 234,984 | G→T | 18.2% | I80I (ATC→ATA) ‡ | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 234,985 | A→T | 8.4% | I80N (ATC→AAC) ‡ | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 234,990 | G→T | 13.8% | F78L (TTC→TTA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 234,994 | G→T | 26.6% | S77* (TCA→TAA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 235,005 | C→A | 17.0% | T73T (ACG→ACT) ‡ | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 235,006 | G→T | 17.3% | T73K (ACG→AAG) ‡ | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 235,010 | G→T | 21.1% | L72I (CTT→ATT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 235,019 | C→A | 29.6% | V69L (GTA→TTA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 235,022 | G→T | 24.7% | H68N (CAT→AAT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 235,036 | G→T | 19.2% | S63Y (TCC→TAC) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 295,695 | T→G | 25.4% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
RA | 345,428 | T→C | 5.6% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
RA | 353,486 | A→T | 8.2% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
RA | 353,489 | C→T | 7.7% | intergenic (+324/+13) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
RA | 353,537 | T→C | 5.2% | K289E (AAA→GAA) | cynR ← | transcriptional activator of cyn operon; autorepressor |
RA | 360,156 | C→G | 7.5% | intergenic (‑90/+505) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
RA | 360,157 | T→G | 7.2% | intergenic (‑91/+504) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
RA | 360,172 | T→A | 5.3% | intergenic (‑106/+489) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
RA | 360,173 | C→A | 9.6% | intergenic (‑107/+488) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
RA | 360,181 | G→C | 5.3% | intergenic (‑115/+480) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
RA | 360,752 | A→G | 100% | V331A (GTG→GCG) | lacI ← | DNA‑binding transcriptional repressor |
JC | 361,139 | +GCCA | 9.7% | coding (605/1083 nt) | lacI ← | DNA‑binding transcriptional repressor |
RA | 361,806 | G→A | 100% | intergenic (‑63/+14) | lacI ← / ← mhpR | DNA‑binding transcriptional repressor/mhp operon transcriptional activator |
RA | 370,632 | A→G | 5.0% | intergenic (+295/‑283) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
RA | 370,703 | A→G | 5.0% | intergenic (+366/‑212) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
RA | 613,891 | T→A | 8.7% | L61Q (CTG→CAG) | fepE → | regulator of length of O‑antigen component of lipopolysaccharide chains |
RA | 667,017 | T→G | 18.1% | E15D (GAA→GAC) | holA ← | DNA polymerase III, delta subunit |
RA | 772,664 | A→C | 7.1% | K289N (AAA→AAC) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
RA | 877,980 | G→T | 5.3% | Q71K (CAA→AAA) | deoR ← | deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx |
RA | 1,191,676 | C→T | 5.1% | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
RA | 1,212,582 | C→A | 10.1% | intergenic (+130/‑202) | ymgC → / → ycgG | Blue light, low temperature and stress induced protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
RA | 1,282,430 | C→T | 6.4% | intergenic (+448/+92) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
JC JC | 1,376,043 | IS5 (–) +4 bp | 100% | pseudogene (10‑13/126 nt) | ycjV → | pseudogene; putative ATP‑binding component of a transport system |
JC JC | 1,427,903 | IS3 (–) +3 bp | 15.1% | coding (27‑29/591 nt) | pinR ← | Rac prophage; putative site‑specific recombinase |
RA | 1,429,253 | G→T | 7.6% | pseudogene (13/51 nt) | ttcC ← | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related |
RA | 1,460,458 | T→C | 5.1% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
RA | 1,460,467 | G→A | 6.0% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
RA | 1,460,887 | G→C | 8.0% | pseudogene (1239/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
RA | 1,460,896 | C→T | 6.9% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
RA | 1,628,207 | G→A | 100% | G110E (GGA→GAA) | pinQ → | Qin prophage; putative site‑specific recombinase |
RA | 1,676,007 | G→C | 6.8% | A94G (GCG→GGG) | ydgC ← | GlpM family inner membrane protein |
RA | 1,702,919 | C→G | 5.6% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
RA | 1,702,966 | T→A | 10.3% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
RA | 1,985,173 | A→T | 6.6% | intergenic (‑73/+123) | yecA ← / ← leuZ | UPF0149 family protein/tRNA‑Leu |
RA | 2,036,746 | G→T | 7.3% | intergenic (+367/+203) | yodB → / ← serU | cytochrome b561 homolog/tRNA‑Ser |
RA | 2,170,707 | C→A | 22.0% | intergenic (‑24/+284) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,170,709 | A→T | 8.2% | intergenic (‑26/+282) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,170,713 | C→A | 25.5% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,170,720 | T→A | 8.2% | intergenic (‑37/+271) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,170,724 | G→T | 25.3% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,170,757 | T→A | 11.4% | intergenic (‑74/+234) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,178,919 | G→T | 6.7% | intergenic (‑139/+84) | thiM ← / ← rcnR | hydoxyethylthiazole kinase/transcriptional repressor of rcnA |
RA | 2,178,937 | A→T | 8.5% | intergenic (‑157/+66) | thiM ← / ← rcnR | hydoxyethylthiazole kinase/transcriptional repressor of rcnA |
RA | 2,298,128 | C→T | 7.5% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
RA | 2,400,223 | A→C | 7.9% | intergenic (‑103/‑817) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
RA | 2,463,906 | C→A | 19.1% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
RA | 2,463,910 | G→T | 18.9% | R434I (AGA→ATA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
RA | 2,463,915 | C→A | 14.3% | Q436K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
RA | 2,587,434 | T→A | 6.8% | L595F (TTA→TTT) | tmcA ← | elongator methionine tRNA (ac4C34) acetyltransferase |
RA | 2,598,122 | T→G | 9.0% | L306R (CTT→CGT) | hyfC → | hydrogenase 4, membrane subunit |
RA | 2,719,168 | A→T | 6.3% | intergenic (‑63/+260) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
RA | 2,785,712 | C→A | 14.8% | H361N (CAC→AAC) | gabD → | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
RA | 2,811,275 | T→G | 6.8% | intergenic (‑56/+143) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
RA | 2,834,252 | A→T | 6.9% | E457V (GAG→GTG) | ascF → | fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component |
RA | 2,908,686 | G→T | 18.2% | E91* (GAA→TAA) | barA → | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
RA | 3,039,409 | T→G | 16.1% | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex |
RA | 3,080,755 | T→G | 26.1% | F231V (TTC→GTC) | metK → | S‑adenosylmethionine synthetase |
RA | 3,203,148 | T→G | 12.9% | K252T (AAG→ACG) | tsaD ← | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein |
RA | 3,385,487 | A→T | 6.2% | intergenic (‑100/+330) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
RA | 3,385,696 | T→A | 6.3% | intergenic (‑309/+121) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
RA | 3,416,890 | T→G | 5.2% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
RA | 3,439,422 | G→T | 7.9% | I26I (ATC→ATA) | rplF ← | 50S ribosomal subunit protein L6 |
RA | 3,498,214 | T→G | 11.1% | intergenic (+72/+80) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
RA | 3,519,657 | G→T | 100% | intergenic (‑149/‑171) | nudE ← / → yrfF | adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein |
RA | 3,602,056 | T→G | 6.8% | intergenic (+47/+55) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
RA | 3,602,367 | T→A | 9.2% | intergenic (‑11/‑210) | tusA ← / → yhhQ | mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase/DUF165 family inner membrane protein |
RA | 3,779,316 | G→T | 9.6% | D233Y (GAT→TAT) | gpmM → | phosphoglycero mutase III, cofactor‑independent |
RA | 3,807,003 | G→T | 5.0% | V305F (GTT→TTT) | dfp → | fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding |
RA | 3,816,601 | A→T | 100% | H281L (CAC→CTC) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
RA | 3,822,339 | A→C | 7.6% | Q12P (CAA→CCA) | xanP → | xanthine permease |
RA | 3,901,867 | T→G | 6.5% | intergenic (‑141/+42) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
RA | 3,960,036 | G→A | 86.5% | R87H (CGC→CAC) | rho → | transcription termination factor |
RA | 4,143,375 | A→G | 6.5% | intergenic (‑349/+249) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
RA | 4,285,857 | T→C | 5.9% | intergenic (+135/+396) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
RA | 4,285,892 | A→G | 5.4% | intergenic (+170/+361) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
RA | 4,297,846 | C→A | 74.2% | M150I (ATG→ATT) | alsE ← | allulose‑6‑phosphate 3‑epimerase |
RA | 4,603,125 | A→C | 7.9% | T300P (ACG→CCG) | yjjU → | putative patatin‑like family phospholipase |
RA | 4,604,320 | T→C | 5.0% | intergenic (+243/+177) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
RA | 4,604,397 | G→A | 5.2% | intergenic (+320/+100) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | CP009273 | 373874 | 375100 | 1227 | 140 [138] | [139] 148 | frmA–[frmR] | frmA,[frmR] |
* | * | ÷ | CP009273 | 4100616 | 4101519 | 904 | 140 [138] | [137] 140 | tpiA | tpiA |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | CP009273 | 360104 = | 176 (0.780) | 125 (0.560) | 81/276 | NT | 41.5% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
* | ? | CP009273 | = 360278 | NA (NA) | 22160 (104.820) +TTAATTAA |
197/260 | NT | 99.0% | intergenic (‑212/+383) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
? | CP009273 | = 361823 | 228 (1.020) | coding (831/834 nt) | mhpR | mhp operon transcriptional activator | |||||
* | ? | CP009273 | 360652 = | 229 (1.020) | 20692 (138.750) +46 bp |
184/184 | NT | 99.3% | intergenic (‑586/+9) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
? | CP009273 | = 1317577 | 184 (0.820) | coding (101/882 nt) | yciV | PHP domain protein | |||||
* | ? | CP009273 | 376716 = | NA (NA) | 153 (0.680) | 102/276 | NT | 75.0% | intergenic (‑1/‑91) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA |
? | CP009273 | 566411 = | 51 (0.230) | coding (63/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
* | ? | CP009273 | = 378046 | NA (NA) | 182 (0.810) | 107/276 | NT | 77.8% | intergenic (+11/+1) | insD1/yaiX | IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase |
? | CP009273 | = 566415 | 52 (0.230) | coding (67/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
* | ? | CP009273 | 776825 = | 113 (0.500) | 19 (0.090) +G |
4/274 | NT | 12.4% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
? | CP009273 | = 2514487 | 157 (0.700) | noncoding (215/1345 nt) | IS186 | repeat region | |||||
* | ? | CP009273 | = 776902 | 131 (0.580) | 7 (0.040) | 4/236 | NT | 5.5% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
? | CP009273 | 2514846 = | 130 (0.680) | noncoding (574/1345 nt) | IS186 | repeat region | |||||
* | ? | CP009273 | 1203246 = | 13 (0.060) | 158 (0.800) | 87/244 | NT | 93.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | CP009273 | 1205075 = | 12 (0.060) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | CP009273 | = 1203261 | 13 (0.060) | 177 (0.890) | 102/244 | NT | 93.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | CP009273 | = 1205058 | 12 (0.060) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | CP009273 | = 2007609 | 220 (0.980) | 32 (0.150) | 23/264 | NT | 14.7% | coding (900/1659 nt) | fliF | flagellar basal‑body MS‑ring and collar protein |
? | CP009273 | 2021385 = | 162 (0.750) | coding (114/1695 nt) | yedQ | putative membrane‑anchored diguanylate cyclase | |||||
* | ? | CP009273 | = 2811301 | 153 (0.680) | 8 (0.040) | 5/236 | NT | 5.3% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
? | CP009273 | 2811851 = | 155 (0.810) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
* | ? | CP009273 | 4532499 = | 114 (0.510) | 84 (0.400) | 53/258 | NT | 44.6% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
? | CP009273 | 4532813 = | 102 (0.490) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
* | ? | CP009273 | = 4532507 | 119 (0.530) | 82 (0.390) | 54/258 | NT | 43.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
? | CP009273 | = 4532803 | 102 (0.490) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |