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 | 123,466 | T→G | 23.6% | A150A (GCT→GCG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 153,122 | C→A | 11.7% | A769S (GCT→TCT) | htrE ← | putative fimbrial usher protein HtrE |
| RA | 183,448 | C→T | 5.3% | A329V (GCG→GTG) | cdaR → | DNA‑binding transcriptional activator CdaR |
| RA | 238,523 | G→T | 19.0% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 29.2% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 325,239 | G→T | 9.7% | I42I (ATC→ATA) | ykgH ← | uncharacterized protein YkgH |
| RA | 347,418 | C→T | 6.2% | V342V (GTG→GTA) | prpR ← | DNA‑binding transcriptional dual regulator PrpR |
| RA | 388,565 | C→T | 5.1% | A257A (GCC→GCT) | tauD → | taurine dioxygenase |
| RA | 444,769 | T→G | 19.7% | R29R (CGT→CGG) | yajQ → | nucleotide binding protein |
| RA | 454,877 | A→T | 61.6% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,883 | C→G | 35.5% | intergenic (+94/‑250) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 580,628 | C→G | 7.0% | intergenic (‑183/‑206) | ylcI ← / → nohD | DLP12 prophage; DUF3950 domain‑containing protein YlcI/DLP12 prophage; putative DNA‑packaging protein NohD |
| RA | 699,874 | A→C | 10.7% | G151G (GGT→GGG) | umpH ← | UMP phosphatase |
| RA | 729,372 | A→C | 23.7% | intergenic (+32/‑211) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 929,492 | C→T | 5.2% | A491T (GCG→ACG) | cydD ← | glutathione/L‑cysteine ABC exporter subunit CydD |
| RA | 937,228 | G→T | 19.4% | intergenic (+15/‑144) | ftsK → / → lolA | cell division DNA translocase FtsK/outer membrane lipoprotein carrier protein |
| RA | 1,053,016 | T→C | 7.9% | K116R (AAG→AGG) | yccM ← | putative 4Fe‑4S membrane protein |
| RA | 1,117,362 | G→A | 6.0% | E186K (GAG→AAG) | yceA → | UPF0176 protein YceA |
| RA | 1,160,101 | G→C | 5.4% | T484S (ACT→AGT) | fhuE ← | ferric coprogen/ferric rhodotorulic acid outer membrane transporter |
| RA | 1,227,487 | T→A | 5.0% | intergenic (‑15/‑194) | pliG ← / → ycgL | inhibitor of g‑type lysozyme/PF05166 family protein YcgL |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,324,213 | C→T | 6.8% | A39V (GCG→GTG) | yciO → | putative RNA‑binding protein YciO |
| RA | 1,340,605 | C→A | 7.2% | G16G (GGC→GGA) | lapB → | lipopolysaccharide assembly protein B |
| RA | 1,361,012 | T→C | 8.8% | intergenic (‑104/‑108) | puuA ← / → puuD | glutamate‑putrescine ligase/gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,399,005 | G→A | 8.9% | I174I (ATC→ATT) | fnr ← | DNA‑binding transcriptional dual regulator FNR |
| RA | 1,411,398 | A→G | 6.7% | V184A (GTT→GCT) | ttcA ← | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| RA | 1,422,998 | G→T | 9.4% | D83Y (GAT→TAT) | ydaW → | Rac prophage; putative uncharacterized protein YdaW |
| RA | 1,425,583 | G→T | 21.9% | M69I (ATG→ATT) | ynaK → | Rac prophage; ParB‑like nuclease domain‑containing protein YnaK |
| RA | 1,434,986 | C→A | 14.6% | pseudogene (23/51 nt) | ttcC ← | putative tRNA 2‑thiocytidine (s(2)C32) synthase |
| RA | 1,455,741 | C→T | 5.1% | A193V (GCA→GTA) | paaC → | phenylacetyl‑CoA 1,2‑epoxidase, structural subunit |
| RA | 1,642,447 | G→T | 11.1% | intergenic (+236/+42) | ynfS → / ← ydfT | Qin prophage; protein YnfS/Qin prophage; putative antitermination protein Q |
| RA | 1,693,416 | A→C | 29.6% | L283R (CTG→CGG) | uidB ← | glucuronide:H(+) symporter |
| RA | 1,713,181 | C→A | 21.0% | S138Y (TCT→TAT) | dtpA → | dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,762,208 | G→T | 100% | A102E (GCA→GAA) | sufC ← | Fe‑S cluster scaffold complex subunit SufC |
| RA | 1,766,646 | C→T | 7.5% | S680S (TCG→TCA) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,820,039 | C→T | 5.4% | M392I (ATG→ATA) | chbC ← | N,N'‑diacetylchitobiose‑specific PTS enzyme IIC component |
| RA | 1,902,343 | T→A | 8.7% | V99E (GTG→GAG) | manX → | mannose‑specific PTS enzyme IIAB component |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,147,842 | C→T | 5.3% | P57S (CCG→TCG) | yegD → | HSP70 family protein YegD |
| 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 | 41.2% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 63.8% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,272 | T→A | 22.5% | intergenic (‑68/+240) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,314,181 | G→T | 21.6% | D232Y (GAT→TAT) | rcsD → | RcsD phosphotransferase |
| RA | 2,458,024 | C→G | 7.7% | G379A (GGA→GCA) | fadJ ← | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| RA | 2,458,780 | A→C | 13.4% | V127G (GTT→GGT) | fadJ ← | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| RA | 2,470,431 | G→T | 52.1% | R434I (AGA→ATA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,436 | C→A | 38.0% | Q436K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,441 | C→A | 36.4% | D437E (GAC→GAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,451 | G→T | 33.4% | V441L (GTA→TTA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,575,892 | T→C | 5.8% | intergenic (‑87/+206) | eutS ← / ← maeB | putative structural protein, ethanolamine utilization microcompartment/malate dehydrogenase |
| RA | 2,663,525 | T→G | 19.1% | A28A (GCT→GCG) | suhB → | inositol‑phosphate phosphatase |
| RA | 2,720,507 | T→A | 7.6% | D185E (GAT→GAA) | patZ → | peptidyl‑lysine acetyltransferase |
| RA | 2,753,306 | T→C | 5.2% | F504F (TTT→TTC) | recN → | DNA repair protein RecN |
| RA | 2,858,941 | A→G | 8.2% | M617V (ATG→GTG) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,866,685 | T→C | 8.2% | E289E (GAA→GAG) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,924,606 | G→T | 8.7% | intergenic (‑82/+129) | csrB ← / ← syd | small regulatory RNA CsrB/SecY‑interacting protein |
| RA | 3,080,613 | C→T | 5.6% | A341A (GCG→GCA) | tktA ← | transketolase 1 |
| RA | 3,134,368 | Δ1 bp | 7.1% | coding (238/693 nt) | yghT → | putative ATP‑binding protein YghT |
| RA | 3,285,605 | A→G | 9.8% | K43R (AAA→AGA) | agaD → | galactosamine‑specific PTS enzyme IID component |
| RA | 3,418,500 | T→A | 30.8% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,418,509 | G→T | 20.4% | M40I (ATG→ATT) | yhdV → | lipoprotein YhdV |
| RA | 3,454,069 | G→T | 17.5% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,495,278 | A→G | 5.9% | Q423R (CAA→CGA) | nirB → | nitrite reductase catalytic subunit NirB |
| RA | 3,497,015 | A→G | 5.2% | T5A (ACT→GCT) | nirC → | nitrite transporter NirC |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,659,576 | C→T | 5.9% | A115A (GCC→GCT) | mdtE → | multidrug efflux pump membrane fusion protein MdtE |
| RA | 3,689,365 | A→C | 9.4% | G299G (GGT→GGG) | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,689,554 | T→C | 10.3% | K236K (AAA→AAG) | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,705,285 | A→C | 14.0% | V169G (GTG→GGG) | dppB ← | dipeptide ABC transporter membrane subunit DppB |
| RA | 3,750,801 | A→C | 22.3% | intergenic (+20/+327) | sgbE → / ← yiaT | L‑ribulose‑5‑phosphate 4‑epimerase SgbE/outer membrane protein YiaT |
| RA | 3,761,313 | T→A | 6.4% | intergenic (‑64/+34) | selA ← / ← yibF | selenocysteine synthase/glutathione transferase‑like protein YibF |
| JC | 3,815,859 | Δ82 bp | 67.4% | [rph] | [rph] | |
| RA | 3,904,699 | A→T | 6.7% | F300Y (TTC→TAC) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| RA | 3,957,617 | G→A | 7.8% | A68A (GCC→GCT) | ilvY ← | DNA‑binding transcriptional dual regulator IlvY |
| RA | 4,059,425 | T→A | 16.8% | V340E (GTA→GAA) | bipA → | ribosome‑dependent GTPase, ribosome assembly factor |
| RA | 4,149,425 | C→T | 5.4% | V281I (GTA→ATA) | eptC ← | phosphoethanolamine transferase EptC |
| RA | 4,188,513 | G→T | 74.5% | G1055V (GGT→GTT) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,283,228 | T→G | 54.9% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,283,230 | A→C | 34.7% | intergenic (‑155/+23) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,283,235 | A→C | 32.7% | intergenic (‑160/+18) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 25.9% | 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 |
| RA | 4,300,906 | A→T | 5.7% | I42N (ATC→AAC) | mdtP ← | putative multidrug efflux pump outer membrane channel |
| RA | 4,398,407 | G→C | 34.8% | Q332H (CAG→CAC) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,533,890 | T→C | 5.0% | K55R (AAA→AGA) | topAI ← | KpLE2 phage‑like element; toxin of the TopAI‑YjhQ toxin‑antitoxin system, TopA inhibitor |
| RA | 4,593,905 | G→A | 5.4% | A273V (GCG→GTG) | lgoT ← | galactonate:H(+) symporter |
| RA | 4,616,474 | C→T | 5.9% | D198N (GAT→AAT) | yjjI ← | DUF3029 domain‑containing protein YjjI |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423753–3424233 | 3424539–3424238 | 6–787 | 19 [18] | [18] 19 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 32 (0.540) | 26 (0.510) | 22/206 | NT | 52.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 19 (0.370) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 28 (0.470) | 24 (0.470) | 19/206 | NT | 52.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 19 (0.370) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 3384720 | 1 (0.020) | 71 (1.200) | 46/236 | NT | 96.0% | coding (18/471 nt) | argR | DNA‑binding transcriptional dual regulator ArgR |
| ? | NC_000913 | 3385156 = | 5 (0.080) | coding (454/471 nt) | argR | DNA‑binding transcriptional dual regulator ArgR | |||||