mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 374,972 | T→C | 6.0% | intergenic (+91/‑487) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 449,555 | T→A | 5.4% | I363F (ATC→TTC) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 466,365 | A→G | 4.1% | H316H (CAT→CAC) | ybaE ← | putative ABC transporter periplasmic binding protein |
| RA | 635,282 | A→G | 6.3% | I32T (ATC→ACC) | ybdM ← | Spo0J family protein, ParB‑like nuclease domain |
| RA | 702,331 | Δ1 bp | 12.3% | coding (421/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 702,583 | C→A | 4.8% | D57Y (GAT→TAT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 891,341 | A→T | 3.8% | D53V (GAC→GTC) | nfsA → | nitroreductase A, NADPH‑dependent, FMN‑dependent |
| RA | 1,158,187 | G→T | 4.4% | E107* (GAA→TAA) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,158,377:1 | +A | 10.6% | coding (509/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| JC | 1,159,286:1 | +GTA | 19.2% | coding (1418/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,290,875 | G→A | 5.5% | G212S (GGC→AGC) | rssB → | PcnB‑degradosome interaction factor, response regulator |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,466,201 | T→C | 7.9% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,665,957 | A→G | 5.4% | T215A (ACG→GCG) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,708,844 | C→G | 9.1% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,726,390 | G→T | 41.5% | R123L (CGC→CTC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 2,037,776 | T→C | 4.5% | D126G (GAT→GGT) | yedV ← | putative sensory kinase in two‑component regulatory system with YedW |
| RA | 2,043,280 | A→T | 3.3% | intergenic (+382/+188) | yodB → / ← serU | cytochrome b561 homolog/tRNA‑Ser |
| JC | 2,059,232 | Δ3 bp | 3.3% | coding (457‑459/1488 nt) | yeeO ← | putative multdrug exporter, MATE family |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,304,796 | T→C | 9.3% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,411,867 | A→G | 4.7% | I74T (ATC→ACC) | yfbT ← | sugar phosphatas |
| RA | 3,051,157 | G→A | 4.5% | R387C (CGC→TGC) | ubiI ← | 2‑octaprenylphenol hydroxylase, FAD‑dependent |
| RA | 3,269,954 | T→C | 13.9% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,318,226 | G→T | 3.4% | noncoding (62/77 nt) | metY ← | tRNA‑Met |
| RA | 3,450,091 | G→A | 2.9% | V47V (GTC→GTT) | rplV ← | 50S ribosomal subunit protein L22 |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 3,909,311 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| 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 | 30.2% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 28.5% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 16.7% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,363,723 | T→C | 3.1% | T441A (ACC→GCC) | dsbD ← | thiol:disulfide interchange protein and activator of DsbC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 4110683 | 4111540 | 858 | 38 [37] | [37] 38 | [cdh]–tpiA | [cdh], tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 193444 = | 88 (0.940) | 3 (0.030) | 3/498 | NT | 3.1% | intergenic (+15/‑77) | frr/dxr | ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase |
| ? | NC_000913 | 193489 = | 105 (1.160) | intergenic (+60/‑32) | frr/dxr | ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 54 (0.570) | 43/518 | NT | 43.9% | 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 | = 700605 | 69 (0.730) | coding (990/1221 nt) | nagC | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 107 (1.140) | 73/518 | 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 | = 258675 | NA (NA) | 33 (0.350) | 29/518 | NT | 31.4% | intergenic (+776/‑1) | 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 | 700597 = | 72 (0.770) | coding (998/1221 nt) | nagC | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor | |||||
| * | ? | NC_000913 | 1207790 = | 45 (0.480) | 39 (0.440) | 31/486 | NT | 45.0% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 53 (0.600) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 42 (0.450) | 39 (0.440) | 34/486 | NT | 45.8% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 53 (0.600) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.010) | 107 (1.140) | 75/518 | NT | 99.1% | 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 | = 1978502 | 0 (0.000) | 47 (0.520) | 38/502 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 45 (0.480) | 32/518 | 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) | 86 (0.910) | 56/518 | 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 | 2582747 = | 96 (1.020) | 3 (0.030) | 3/504 | NT | 2.8% | coding (29/1044 nt) | ypfG | DUF1176 family protein |
| ? | NC_000913 | 2583309 = | 112 (1.220) | coding (168/576 nt) | nudK | GDP‑mannose pyrophosphatase | |||||