mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 374,986 | T→C | 3.1% | intergenic (+105/‑473) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 447,112:1 | +C | 2.6% | coding (594/891 nt) | cyoE ← | protoheme IX farnesyltransferase |
| RA | 451,999 | Δ1 bp | 3.8% | intergenic (‑389/+71) | cyoA ← / ← ampG | cytochrome o ubiquinol oxidase subunit II/muropeptide transporter |
| RA | 638,205 | A→G | 2.6% | D123D (GAT→GAC) | dsbG ← | thiol:disulfide interchange protein, periplasmic |
| RA | 701,381 | (C)5→4 | 100% | coding (214/1221 nt) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 702,331 | Δ1 bp | 22.2% | coding (421/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 764,024 | A→G | 2.8% | A337A (GCA→GCG) | sucC → | succinyl‑CoA synthetase, beta subunit |
| RA | 820,563 | T→C | 3.0% | L227S (TTG→TCG) | ybhL → | putative acetate transporter, BAX Inhibitor‑1 family inner membrane protein |
| RA | 853,374 | G→A | 2.7% | L64L (CTG→CTA) | mntR → | Mn(2+)‑responsive manganese regulon transcriptional regulator |
| RA | 970,394 | G→T | 3.2% | V336F (GTT→TTT) | ycaQ → | DUF1006 family protein with C‑terminal wHTH domain |
| RA | 1,158,383 | G→A | 13.6% | W172* (TGG→TAG) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,269,474 | A→T | 3.7% | intergenic (+85/+229) | rdlA → / ← ldrB | sRNA antisense regulator affects LdrA translation, proposed addiction module in LDR‑A repeat, with toxic peptide LdrA/toxic polypeptide, small |
| RA | 1,269,574 | G→T | 4.1% | intergenic (+185/+129) | rdlA → / ← ldrB | sRNA antisense regulator affects LdrA translation, proposed addiction module in LDR‑A repeat, with toxic peptide LdrA/toxic polypeptide, small |
| RA | 1,287,360 | A→T | 7.0% | intergenic (‑32/+178) | tyrV ← / ← tyrT | tRNA‑Tyr/tRNA‑Tyr |
| RA | 1,335,234 | T→C | 2.8% | G37G (GGT→GGC) | ymiA → | uncharacterized protein |
| RA | 1,387,960 | G→A | 3.3% | G414E (GGA→GAA) | tyrR → | aromatic amino acid biosynthesis and transport regulon transcriptional regulator, autorepressor, ATPase, phosphatase |
| RA | 1,466,438 | T→G | 6.3% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,582 | T→C | 11.4% | pseudogene (1191/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,585 | T→C | 9.5% | pseudogene (1194/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,712 | G→A | 5.6% | pseudogene (1321/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,714 | T→C | 6.5% | pseudogene (1323/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,717 | C→T | 9.3% | pseudogene (1326/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,729 | G→A | 6.2% | pseudogene (1338/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,856 | A→G | 5.2% | pseudogene (1465/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,467,851 | T→A | 3.2% | pseudogene (2460/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,507,045 | T→C | 3.0% | Y89H (TAC→CAC) | ydcP → | putative peptidase |
| RA | 1,579,809 | A→T | 2.8% | C328S (TGT→AGT) | ydeM ← | putative YdeN‑specific sulfatase‑maturating enzyme |
| RA | 1,650,227 | Δ1 bp | 2.9% | pseudogene (150/765 nt) | ydfE → | Qin prophage, pseudogene,Phage or Prophage Related |
| RA | 1,689,853 | T→A | 3.5% | M1K (ATG→AAG) † | ydgA → | DUF945 family protein |
| RA | 1,708,709 | T→C | 10.6% | R597R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,930 | C→A | 8.2% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,726,155 | T→G | 55.5% | F45V (TTC→GTC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,373 | Δ1 bp | 16.7% | coding (351/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,374 | Δ1 bp | 16.7% | coding (352/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| JC | 1,726,492 | Δ4 bp | 17.6% | coding (470‑473/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,528 | G→T | 7.4% | G169V (GGC→GTC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,572:1 | +G | 7.5% | coding (550/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,803,049 | A→T | 2.7% | intergenic (‑479/‑45) | thrS ← / → arpB | threonyl‑tRNA synthetase/pseudogene, ankyrin repeats |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,138,182:1 | +G | 3.1% | coding (281/1584 nt) | yegH → | inner membrane protein |
| RA | 2,168,130 | Δ1 bp | 3.3% | coding (177/318 nt) | yegR ← | uncharacterized protein |
| RA | 2,391,194:1 | +C | 2.9% | coding (310/1458 nt) | nuoN ← | NADH:ubiquinone oxidoreductase, membrane subunit N |
| RA | 2,429,535 | A→G | 3.3% | T234T (ACT→ACC) | purF ← | amidophosphoribosyltransferase |
| RA | 2,458,380 | Δ1 bp | 3.3% | coding (778/2145 nt) | fadJ ← | enoyl‑CoA hydratase/epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase |
| JC | 2,662,349 | Δ182 bp | 3.8% | intergenic (‑220/+51) | iscR ← / ← trmJ | isc operon transcriptional repressor, suf operon transcriptional activator, oxidative stress‑ and iron starvation‑inducible, autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 2,906,674 | G→T | 9.4% | Y422* (TAC→TAA) | eno ← | enolase |
| JC | 3,101,307 | Δ3 bp | 2.5% | coding (313‑315/720 nt) | yggN ← | DUF2884 family putative periplasmic protein |
| RA | 3,133,380 | Δ1 bp | 3.1% | coding (576/714 nt) | yghS ← | putative ATP‑binding protein |
| RA | 3,137,951:1 | +G | 2.5% | coding (570/1860 nt) | gss ← | glutathionylspermidine amidase and glutathionylspermidine synthetase |
| RA | 3,198,335 | Δ1 bp | 2.8% | coding (1305/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,336 | Δ1 bp | 2.8% | coding (1304/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,337 | Δ1 bp | 2.8% | coding (1303/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,338 | Δ1 bp | 2.8% | coding (1302/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,339 | Δ1 bp | 2.8% | coding (1301/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,340 | Δ1 bp | 2.8% | coding (1300/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,341 | Δ1 bp | 2.8% | coding (1299/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,342 | Δ1 bp | 2.7% | coding (1298/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,343 | Δ1 bp | 2.7% | coding (1297/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,347 | Δ1 bp | 2.8% | coding (1293/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,348 | Δ1 bp | 2.8% | coding (1292/2841 nt) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,233,244 | T→G | 10.7% | F528V (TTC→GTC) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,327,207 | A→T | 2.7% | R152R (CGT→CGA) | rlmE ← | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 3,327,210 | A→T | 2.5% | C151* (TGT→TGA) ‡ | rlmE ← | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 3,327,211 | C→G | 2.5% | C151S (TGT→TCT) ‡ | rlmE ← | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 3,327,213 | C→T | 2.6% | M150I (ATG→ATA) | rlmE ← | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 3,334,813 | G→A | 3.6% | intergenic (+134/‑94) | ispB → / → sfsB | octaprenyl diphosphate synthase/malPQ operon transcriptional activator |
| RA | 3,498,080 | T→G | 3.5% | L85L (CTT→CTG) | cysG → | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase |
| RA | 3,498,082 | A→T | 3.1% | N86I (AAC→ATC) | cysG → | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase |
| RA | 3,508,892 | G→A | 6.3% | A307V (GCA→GTA) | yhfW ← | phosphopentomutase‑related metalloenzyme superfamily protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,528 | C→G | 6.3% | S31C (TCC→TGC) | yidX → | putative lipoprotein |
| RA | 3,875,535 | C→A | 8.8% | T33T (ACC→ACA) | yidX → | putative lipoprotein |
| MC JC | 3,909,311 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| RA | 3,938,979 | G→T | 7.4% | G252C (GGC→TGC) | rbsR → | transcriptional repressor of ribose metabolism |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,094,606 | C→T | 3.4% | intergenic (‑335/+116) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,135,644 | T→C | 3.6% | L604P (CTG→CCG) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,171,647 | A→C | 100% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,189 | A→G | 32.2% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 28.6% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 19.2% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,326,089 | T→G | 5.7% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,585,613 | C→T | 3.1% | E384K (GAA→AAA) | hsdR ← | endonuclease R Type I restriction enzyme |
| JC | 4,606,168 | Δ236 bp | 5.0% | leuP–leuQ | leuP, leuQ | |
| RA | 4,621,621 | G→T | 2.7% | intergenic (+18/‑149) | deoD → / → yjjJ | purine nucleoside phosphorylase 1, nicotinamide 1‑beta‑D‑riboside phosphorylase/putative protein kinase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 4110691 | 4111550 | 860 | 64 [61] | [61] 63 | tpiA | tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 225456 = | 70 (0.480) | 8 (0.060) | 5/502 | NT | 8.9% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | 4037236 = | 97 (0.690) | intergenic (+20/‑23) | ileT/alaT | tRNA‑Ile/tRNA‑Ala | |||||
| * | ? | NC_000913 | 228016 = | NA (NA) | 3 (0.020) | 3/506 | NT | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 138 (0.950) | 94/520 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1159285 = | 53 (0.360) | 76 (0.530) | 61/516 | NT | 59.1% | coding (1417/1434 nt) | ptsG | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| ? | NC_000913 | = 1469238 | NA (NA) | intergenic (‑89/‑3) | insC1/ydbA | IS2 repressor TnpA/pseudogene, autotransporter homolog, interrupted by IS2 and IS30 | |||||
| * | ? | NC_000913 | = 1159291 | 51 (0.350) | 69 (0.470) | 54/520 | NT | 57.5% | coding (1423/1434 nt) | ptsG | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| ? | NC_000913 | = 1651548 | 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 | |||||
| * | ? | NC_000913 | 1207790 = | 55 (0.380) | 83 (0.610) | 60/488 | NT | 63.9% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 42 (0.310) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 55 (0.380) | 89 (0.650) | 57/488 | NT | 65.5% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 42 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.010) | 174 (1.190) | 104/520 | NT | 99.4% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 81 (0.560) | 61/512 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 106 (0.730) | 68/520 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 110 (0.750) | 71/520 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 3327191 = | 185 (1.270) | 6 (0.040) | 6/502 | NT | 3.2% | coding (472/630 nt) | rlmE | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent |
| ? | NC_000913 | 3327228 = | 181 (1.290) | coding (435/630 nt) | rlmE | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | = 3498079 | 114 (0.780) | 5 (0.040) | 5/502 | NT | 4.3% | coding (254/1374 nt) | cysG | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase |
| ? | NC_000913 | = 3498084 | 113 (0.800) | coding (259/1374 nt) | cysG | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase | |||||
| * | ? | NC_000913 | 4516892 = | 169 (1.160) | 7 (0.050) | 7/502 | NT | 4.1% | coding (827/954 nt) | fecR | anti‑sigma transmembrane signal transducer for ferric citrate transport, periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| ? | NC_000913 | 4516926 = | 161 (1.140) | coding (793/954 nt) | fecR | anti‑sigma transmembrane signal transducer for ferric citrate transport, periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator | |||||
| * | ? | NC_000913 | 4522459 = | 156 (1.070) | 4 (0.030) | 4/500 | NT | 2.8% | coding (1637/1968 nt) | yjhG | putative dehydratase |
| ? | NC_000913 | 4522502 = | 123 (0.880) | coding (1594/1968 nt) | yjhG | putative dehydratase | |||||