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 | 207,541 | C→T | 6.7% | R806W (CGG→TGG) | dnaE → | DNA polymerase III subunit alpha |
| RA | 238,497 | G→T | 13.5% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,516 | A→T | 16.5% | I74K (ATA→AAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 19.5% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 28.7% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 298,239 | G→A | 10.8% | T163M (ACG→ATG) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 298,557 | A→C | 40.3% | L57R (CTC→CGC) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 388,241 | G→A | 6.6% | L149L (CTG→CTA) | tauD → | taurine dioxygenase |
| RA | 616,090 | G→A | 8.0% | C645Y (TGC→TAC) | entF → | apo‑serine activating enzyme |
| RA | 665,176 | C→T | 6.8% | W5* (TGG→TGA) | rlpA ← | rare lipoprotein RlpA |
| RA | 827,678 | C→T | 16.7% | R435Q (CGG→CAG) | ybhF ← | putative ABC exporter ATP binding subunit |
| RA | 863,171 | A→G | 9.3% | L114P (CTG→CCG) | ybiY ← | putative pyruvate formate‑lyase activating enzyme YbiY |
| RA | 887,746 | G→A | 5.0% | Q108Q (CAG→CAA) | rcdA → | DNA‑binding transcriptional regulator RcdA |
| RA | 916,877 | A→G | 18.5% | G135G (GGA→GGG) | ybjD → | DUF2813 domain‑containing protein YbjD |
| RA | 924,622 | C→T | 5.6% | G453G (GGC→GGT) | clpA → | ATP‑dependent Clp protease ATP‑binding subunit ClpA |
| RA | 972,545 | A→T | 17.8% | Y265F (TAT→TTT) | ycbJ → | putative phosphotransferase YcbJ |
| RA | 995,958 | T→G | 17.7% | T11P (ACC→CCC) | ssuD ← | FMNH2‑dependent alkanesulfonate monooxygenase |
| RA | 1,020,574 | T→G | 6.1% | I116L (ATC→CTC) | sulA ← | cell division inhibitor SulA |
| RA | 1,157,593 | C→T | 100% | intergenic (+19/‑276) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
| RA | 1,178,828 | A→G | 40.0% | N79S (AAT→AGT) | nagK → | N‑acetyl‑D‑glucosamine kinase |
| RA | 1,253,997 | T→G | 16.4% | K652N (AAA→AAC) | ycgV ← | putative autotransporter adhesin YcgV |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,341,896 | T→C | 26.1% | intergenic (+169/‑25) | lapB → / → pyrF | lipopolysaccharide assembly protein B/orotidine‑5'‑phosphate decarboxylase |
| RA | 1,435,245 | G→A | 6.4% | L125L (CTC→CTT) | uspF ← | nucleotide binding filament protein |
| RA | 1,441,455 | G→T | 9.1% | Q97K (CAG→AAG) | hslJ ← | lipoprotein implicated in Novobiocin resistance |
| RA | 1,705,120 | G→T | 16.0% | D58Y (GAC→TAC) | cnu → | H‑NS‑ and StpA‑binding protein |
| RA | 1,792,362 | G→T | 23.8% | Q124K (CAA→AAA) | nlpC ← | NlpC/P60 family lipoprotein NlpC |
| RA | 1,839,671 | T→A | 6.9% | L69I (TTA→ATA) | ynjE → | molybdopterin synthase sulfurtransferase |
| RA | 1,843,410 | C→T | 7.7% | A347V (GCA→GTA) | gdhA → | glutamate dehydrogenase |
| RA | 1,875,748 | Δ1 bp | 5.7% | coding (76/1182 nt) | nimT → | 2‑nitroimidazole exporter |
| RA | 1,887,464 | T→C | 13.5% | L176L (CTA→CTG) | rnd ← | RNase D |
| RA | 1,917,265 | G→A | 9.5% | L336L (CTG→CTA) | yebS → | intermembrane transport protein YebS |
| RA | 1,956,306 | T→C | 6.8% | E234E (GAA→GAG) | torZ ← | trimethylamine N‑oxide reductase 2 |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,984,760 | A→G | 7.0% | Y104H (TAT→CAT) | araG ← | arabinose ABC transporter ATP binding subunit |
| RA | 2,043,929 | T→C | 6.9% | Y93Y (TAT→TAC) | mtfA → | Mlc titration factor |
| RA | 2,139,584 | A→T | 21.7% | intergenic (+99/+175) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,139,598 | T→G | 33.8% | intergenic (+113/+161) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,163,154 | A→C | 13.7% | K93N (AAA→AAC) | baeS → | sensory histidine kinase BaeS |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,234 | C→A | 51.6% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 47.9% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,279 | C→A | 18.9% | intergenic (‑75/+233) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,225,351 | G→A | 5.3% | A94V (GCG→GTG) | yohC ← | putative inner membrane protein |
| RA | 2,313,866 | C→T | 5.0% | R127W (CGG→TGG) | rcsD → | RcsD phosphotransferase |
| RA | 2,324,245 | A→G | 5.2% | E46G (GAA→GGA) | atoA → | acetyl‑CoA:acetoacetyl‑CoA transferase subunit beta |
| RA | 2,470,427 | C→A | 36.9% | Q433K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,435 | T→A | 21.2% | N435K (AAT→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,463 | G→T | 39.2% | intergenic (+1/+614) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,579,830 | C→T | 6.5% | H65H (CAC→CAT) | tktB → | transketolase 2 |
| RA | 2,642,521 | T→G | 34.1% | K108N (AAA→AAC) | rodZ ← | transmembrane component of cytoskeleton |
| RA | 2,669,722 | G→A | 6.7% | G231S (GGC→AGC) | hcaE → | putative 3‑phenylpropionate/cinnamate dioxygenase subunit alpha |
| RA | 2,673,429 | C→A | 24.4% | F28L (TTC→TTA) | yphA → | putative inner membrane protein |
| RA | 2,725,790 | T→G | 24.8% | intergenic (‑44/+279) | kgtP ← / ← rrfG | alpha‑ketoglutarate:H(+) symporter/5S ribosomal RNA |
| RA | 2,734,581 | A→T | 8.3% | W152R (TGG→AGG) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,775,547 | G→T | 17.4% | pseudogene (3/272 nt) | ypjI → | putative UPF0401 protein YpjI |
| RA | 2,925,321 | A→T | 18.1% | intergenic (‑41/‑27) | syd ← / → queF | SecY‑interacting protein/7‑cyano‑7‑deazaguanine reductase |
| RA | 3,015,469 | A→G | 5.9% | T104A (ACC→GCC) | mocA → | molybdenum cofactor cytidylyltransferase |
| RA | 3,216,234 | A→C | 34.3% | R86R (CGT→CGG) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | 3,377,145 | G→T | 10.6% | Y92* (TAC→TAA) | sspA ← | stringent starvation protein A |
| RA | 3,377,215 | A→G | 33.3% | L69P (CTG→CCG) | sspA ← | stringent starvation protein A |
| RA | 3,454,069 | G→T | 48.7% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,511,857 | G→A | 5.9% | P163L (CCG→CTG) | yhfZ ← | putative DNA‑binding transcriptional regulator YhfZ |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,612,271 | T→C | 6.8% | F136S (TTC→TCC) | yhhT → | putative transporter YhhT |
| RA | 3,617,735 | G→A | 23.3% | V241I (GTT→ATT) | nikD → | Ni(2(+)) ABC transporter ATP binding subunit NikD |
| RA | 3,877,635 | C→A | 34.2% | intergenic (‑170/+70) | yidB ← / ← gyrB | conserved protein YidB/DNA gyrase subunit B |
| RA | 3,882,526 | A→C | 22.2% | S402A (TCG→GCG) | dnaA ← | chromosomal replication initiator protein DnaA |
| RA | 4,028,235 | T→G | 22.8% | T180P (ACG→CCG) | fadA ← | 3‑ketoacyl‑CoA thiolase |
| RA | 4,086,065 | G→T | 6.1% | G17V (GGT→GTT) | fdhD → | sulfurtransferase for molybdenum cofactor sulfuration |
| JC JC | 4,118,284 | IS5 (–) +4 bp | 36.4% | intergenic (‑194/‑228) | glpF ← / → zapB | glycerol facilitator/cell division factor ZapB |
| RA | 4,124,554 | T→C | 5.5% | intergenic (‑98/+58) | cytR ← / ← priA | DNA‑binding transcriptional repressor CytR/primosome factor N' |
| RA | 4,174,723 | T→C | 5.7% | S102G (AGT→GGT) | coaA ← | pantothenate kinase |
| JC | 4,181,657 | (CAACGGTACCTTTGTTAT)1→2 | 59.9% | coding (413/4029 nt) | rpoB → | RNA polymerase subunit beta |
| RA | 4,185,894 | C→T | 30.5% | A182V (GCG→GTG) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,200,338 | C→T | 7.9% | Q20* (CAG→TAG) | hupA → | DNA‑binding protein HU‑alpha |
| JC | 4,200,420 | Δ10 bp | 7.5% | coding (140‑149/273 nt) | hupA → | DNA‑binding protein HU‑alpha |
| RA | 4,283,228 | T→G | 45.8% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 29.0% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| JC | 4,397,611 | +GCTGGC | 42.6% | coding (200/1848 nt) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,404,645 | C→T | 6.0% | intergenic (+62/‑42) | yjeT → / → purA | DUF2065 domain‑containing protein YjeT/adenylosuccinate synthetase |
| RA | 4,489,240 | G→A | 16.7% | A275V (GCC→GTC) | yjgR ← | DUF853 domain‑containing protein YjgR |
| RA | 4,591,497 | Δ1 bp | 5.3% | intergenic (‑218/‑160) | btsT ← / → tsr | pyruvate:H(+) symporter/methyl‑accepting chemotaxis protein Tsr |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423762–3424234 | 3424551–3424238 | 5–790 | 16 [15] | [15] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3486119 | 3486774 | 656 | 17 [14] | [15] 16 | crp | crp |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 24 (0.430) | 36 (0.740) | 29/204 | NT | 63.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 20 (0.410) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.410) | 28 (0.570) | 24/204 | NT | 58.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 20 (0.410) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 37 (0.660) | 4 (0.080) | 4/218 | NT | 7.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 63 (1.210) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||