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 | position | mutation | freq | annotation | gene | description |
| RA | 27,603 | T→G | 7.9% | F104C (TTT→TGT) | rihC → | ribonucleoside hydrolase 3 |
| JC | 89,331 | Δ3 bp | 5.1% | coding (1432‑1434/1767 nt) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis (penicillin‑binding protein 3) |
| RA | 161,068 | A→C | 31.1% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 191,749 | G→T | 7.3% | L120F (TTG→TTT) | ispU → | undecaprenyl pyrophosphate synthase |
| RA | 234,994 | G→T | 11.8% | S77* (TCA→TAA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,010 | G→T | 11.0% | L72I (CTT→ATT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,019 | C→A | 13.3% | V69L (GTA→TTA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 235,022 | G→T | 16.5% | H68N (CAT→AAT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 295,695 | T→G | 18.2% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 297,724 | A→C | 10.4% | D187E (GAT→GAG) | paoA ← | PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit |
| RA | 353,486 | A→T | 5.2% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 360,173 | C→A | 5.4% | intergenic (‑107/+488) | 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 | 68.1% | 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 | 450,333 | A→T | 9.8% | intergenic (+88/‑256) | bolA → / → tig | stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor) |
| RA | 725,273 | A→C | 8.6% | S79R (AGC→CGC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 772,664 | A→C | 12.5% | K289N (AAA→AAC) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
| JC JC | 919,057 | IS5 (–) +4 bp | 18.4% | coding (338‑341/2277 nt) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 1,118,506 | A→T | 8.2% | L75Q (CTA→CAA) | yceB ← | lipoprotein, DUF1439 family |
| RA | 1,147,909 | G→A | 11.0% | G172D (GGC→GAC) | fabF → | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| JC | 1,191,242 | +GTGACTCT | 23.9% | coding (664/1251 nt) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,676 | C→T | 5.4% | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,688 | C→T | 5.0% | T370T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,282,421 | A→T | 12.5% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,497 | A→G | 7.0% | intergenic (+515/+25) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,598 | G→T | 5.2% | noncoding (95/171 nt) P12Q (CCA→CAA) ‡ |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,282,599 | G→T | 6.2% | noncoding (94/171 nt) P12T (CCA→ACA) ‡ |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,327,193 | G→T | 7.6% | C630F (TGC→TTC) | topA → | DNA topoisomerase I, omega subunit |
| JC JC | 1,376,043 | IS5 (–) +4 bp | 53.8% | pseudogene (10‑13/126 nt) | ycjV → | pseudogene; putative ATP‑binding component of a transport system |
| RA | 1,460,752 | C→T | 10.0% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,761 | A→G | 7.0% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,588,339 | T→G | 5.1% | pseudogene (3906/5323 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,628,207 | G→A | 57.3% | G110E (GGA→GAA) | pinQ → | Qin prophage; putative site‑specific recombinase |
| RA | 1,673,380 | T→A | 5.7% | S233T (TCA→ACA) | ydgH → | DUF1471 family periplasmic protein |
| RA | 1,702,966 | T→A | 6.9% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,703,062 | T→A | 12.3% | R629R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,703,071 | A→T | 9.8% | A632A (GCA→GCT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,703,101 | C→G | 5.4% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,784,723 | A→C | 9.6% | F260C (TTT→TGT) | ydiU ← | UPF0061 family protein |
| RA | 1,795,380 | A→T | 19.2% | V483E (GTA→GAA) | thrS ← | threonyl‑tRNA synthetase |
| RA | 1,796,428 | C→A | 12.8% | V134F (GTC→TTC) | thrS ← | threonyl‑tRNA synthetase |
| RA | 1,823,843 | A→C | 5.6% | F50C (TTT→TGT) | astD ← | succinylglutamic semialdehyde dehydrogenase |
| RA | 2,170,708 | G→T | 7.5% | intergenic (‑25/+283) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,713 | C→A | 21.0% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,724 | G→T | 22.2% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,758 | C→A | 6.4% | intergenic (‑75/+233) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,298,128 | C→T | 7.4% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,463,906 | C→A | 23.5% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,463,910 | G→T | 13.9% | R434I (AGA→ATA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,463,915 | C→A | 20.5% | Q436K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,463,920 | C→A | 10.8% | D437E (GAC→GAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,711,673 | A→C | 6.3% | V72G (GTT→GGT) | yfiF ← | putative methyltransferase |
| JC | 2,713,645 | +CCTGCGC | 34.6% | coding (334/2661 nt) | pka → | protein lysine acetyltransferase |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,811,405 | A→G | 6.2% | intergenic (‑186/+13) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,811,408 | T→A | 7.0% | intergenic (‑189/+10) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,834,267 | A→T | 6.4% | E462V (GAG→GTG) | ascF → | fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component |
| RA | 2,940,829 | A→T | 6.6% | intergenic (+7/‑27) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 3,039,409 | T→G | 12.1% | 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 | 14.8% | F231V (TTC→GTC) | metK → | S‑adenosylmethionine synthetase |
| RA | 3,263,315 | T→C | 7.4% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,263,895 | T→A | 5.2% | noncoding (57/377 nt) | rnpB ← | RNase P, M1 RNA component |
| RA | 3,385,487 | A→T | 6.5% | intergenic (‑100/+330) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,385,493 | G→T | 8.2% | intergenic (‑106/+324) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,385,516 | A→T | 5.7% | intergenic (‑129/+301) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,385,578 | A→T | 6.7% | intergenic (‑191/+239) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,385,662 | C→G | 6.8% | intergenic (‑275/+155) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,416,890 | T→G | 8.7% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,453,434 | C→A | 6.2% | Q87K (CAA→AAA) | gspF → | general secretory pathway component, cryptic |
| RA | 3,498,214 | T→G | 8.2% | 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 | 3,525,232 | T→A | 10.4% | L189F (TTA→TTT) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,553,919 | T→G | 7.5% | Q16P (CAG→CCG) | glpR ← | GlpR DNA‑binding transcriptional repressor |
| JC | 3,589,657 | Δ9 bp | 7.5% | coding (99‑107/927 nt) | livH ← | leucine/isoleucine/valine transporter subunit |
| RA | 3,721,485 | T→G | 8.3% | Y416S (TAC→TCC) | xylB ← | xylulokinase |
| RA | 3,774,382 | T→G | 7.3% | intergenic (+5/‑193) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,786,682 | C→A | 6.2% | C121F (TGT→TTT) | yibB ← | YibB family protein, function unknown |
| RA | 3,816,601 | A→T | 58.6% | H281L (CAC→CTC) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,816,844 | T→A | 9.7% | L362Q (CTG→CAG) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,822,339 | A→C | 9.7% | Q12P (CAA→CCA) ‡ | xanP → | xanthine permease |
| RA | 3,822,340 | A→C | 13.7% | Q12H (CAA→CAC) ‡ | xanP → | xanthine permease |
| RA | 3,822,345 | T→G | 9.6% | V14G (GTT→GGT) ‡ | xanP → | xanthine permease |
| RA | 3,822,346 | T→G | 6.5% | V14V (GTT→GTG) ‡ | xanP → | xanthine permease |
| RA | 3,872,511 | A→C | 5.6% | V323V (GTT→GTG) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,896,183 | A→C | 8.5% | D293E (GAT→GAG) | bglB ← | cryptic phospho‑beta‑glucosidase B |
| RA | 3,960,036 | G→A | 6.5% | R87H (CGC→CAC) | rho → | transcription termination factor |
| RA | 4,143,375 | A→G | 7.1% | intergenic (‑349/+249) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,208,624 | G→T | 7.4% | R34L (CGT→CTT) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,208,819 | C→T | 9.5% | A99V (GCG→GTG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,315,765 | A→G | 6.4% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,388,233 | A→C | 5.1% | E335D (GAA→GAC) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,603,125 | A→C | 6.5% | T300P (ACG→CCG) | yjjU → | putative patatin‑like family phospholipase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 373857 | 375112 | 1256 | 181 [177] | [179] 185 | frmA–[frmR] | frmA,[frmR] |
| * | * | ÷ | CP009273 | 4100622 | 4101511 | 890 | 185 [179] | [179] 185 | tpiA | tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 274 (0.880) | 204 (0.660) | 120/278 | NT | 42.7% | 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) | 11232 (38.430) +TTAATTAA |
195/262 | NT | 97.6% | intergenic (‑212/+383) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 361823 | 293 (0.940) | coding (831/834 nt) | mhpR | mhp operon transcriptional activator | |||||
| * | ? | CP009273 | 360652 = | 418 (1.350) | 10222 (49.420) +46 bp |
183/186 | NT | 97.8% | intergenic (‑586/+9) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 1317577 | 271 (0.870) | coding (101/882 nt) | yciV | PHP domain protein | |||||
| * | ? | CP009273 | 376716 = | NA (NA) | 12 (0.040) | 8/278 | NT | 6.4% | intergenic (‑1/‑91) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA |
| ? | CP009273 | 1190448 = | 175 (0.560) | intergenic (‑41/‑131) | rluE/icd | 23S rRNA pseudouridine(2457) synthase/e14 prophage; isocitrate dehydrogenase, specific for NADP+ | |||||
| * | ? | CP009273 | = 378046 | NA (NA) | 14 (0.050) | 9/278 | NT | 5.5% | intergenic (+11/+1) | insD1/yaiX | IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase |
| ? | CP009273 | = 566415 | 240 (0.770) | coding (67/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
| * | ? | CP009273 | 1190506 = | 213 (0.690) | 15 (0.050) | 11/278 | NT | 6.6% | intergenic (‑99/‑73) | rluE/icd | 23S rRNA pseudouridine(2457) synthase/e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| ? | CP009273 | = 1645805 | NA (NA) | intergenic (+11/‑3) | insD1/intQ | IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1190510 | 226 (0.730) | 16 (0.050) | 12/278 | NT | 6.6% | intergenic (‑103/‑69) | rluE/icd | 23S rRNA pseudouridine(2457) synthase/e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| ? | CP009273 | = 1463497 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | CP009273 | 1203246 = | 110 (0.350) | 134 (0.490) | 74/246 | NT | 59.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 88 (0.320) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 112 (0.360) | 200 (0.730) | 101/246 | NT | 68.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 88 (0.320) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1282540 | 151 (0.490) | 11 (0.040) | 5/238 | NT | 5.9% | noncoding (153/171 nt) | rttR | rtT sRNA, processed from tyrT transcript |
| ? | CP009273 | 1283013 = | 221 (0.830) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | CP009273 | = 2007609 | 153 (0.490) | 151 (0.510) | 90/266 | NT | 52.7% | coding (900/1659 nt) | fliF | flagellar basal‑body MS‑ring and collar protein |
| ? | CP009273 | 2021385 = | 125 (0.420) | coding (114/1695 nt) | yedQ | putative membrane‑anchored diguanylate cyclase | |||||
| * | ? | CP009273 | = 3180785 | NA (NA) | 23 (0.070) | 16/278 | NT | 7.0% | pseudogene (6/2445 nt) | yqiG | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | CP009273 | = 3904841 | 305 (0.980) | coding (45/1041 nt) | pstS | periplasmic phosphate binding protein, high‑affinity | |||||
| * | ? | CP009273 | 3904837 = | 316 (1.020) | 20 (0.060) | 12/278 | NT | 6.0% | coding (49/1041 nt) | pstS | periplasmic phosphate binding protein, high‑affinity |
| ? | CP009273 | 4487998 = | NA (NA) | intergenic (+241/‑91) | intB/insC1 | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA | |||||
| * | ? | CP009273 | 4532499 = | 142 (0.460) | 46 (0.160) | 33/260 | NT | 23.6% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 165 (0.570) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 4532507 | 138 (0.440) | 50 (0.170) | 34/260 | NT | 25.4% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 165 (0.570) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||