mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 70,434 | C→T | 38.1% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 34.1% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 38.0% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 43.7% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 40.9% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 37.1% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,109 | T→C | 27.9% | T241T (ACT→ACC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,175 | A→G | 43.5% | R263R (CGA→CGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,214 | T→C | 32.7% | F276F (TTT→TTC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 155,463 | A→T | 100% | *247K (TAA→AAA) | ecpD ← | predicted periplasmic pilin chaperone |
| RA | 236,101 | A→C | 45.9% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 43.4% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 547,694 | A→G | 100% | pseudogene (114/261 nt) pseudogene (114/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 547,831:1 | +G | 100% | pseudogene (251/261 nt) pseudogene (251/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 556,858 | A→T | 100% | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| MC JC | 654,214 | Δ1,199 bp | 100% | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 1,093,686 | T→C | 100% | V130A (GTA→GCA) | ycdT → | predicted diguanylate cyclase |
| MC JC | 1,301,041 | Δ1,336 bp | 100% | insC–insD | insC, insD | |
| RA | 1,303,631 | C→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,303,633 | G→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| MC JC | 2,176,983 | Δ1,199 bp | 100% | [gatA]–[gatA] | [gatA], insH, [gatA] | |
| MC JC | 2,320,795 | Δ1,336 bp | 100% | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,809,581 | G→A | 44.9% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 2,855,731 | G→T | 17.8% | intergenic (‑269/‑18) | ygbA ← / → mutS | hypothetical protein/methyl‑directed mismatch repair protein |
| RA | 2,855,732 | G→A | 17.8% | intergenic (‑270/‑17) | ygbA ← / → mutS | hypothetical protein/methyl‑directed mismatch repair protein |
| RA | 2,866,110 | T→A | 100% | intergenic (‑20/+160) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
| MC JC | 3,261,134 | Δ1,199 bp | 100% | insH–[tdcD] | insH, [tdcD] | |
| MC JC | 3,742,938 | Δ1,336 bp | 100% | insD–insC | insD, insC | |
| MC JC | 3,746,913 | Δ1,199 bp | 100% | [tnaB]–[tnaB] | [tnaB], insH, [tnaB] | |
| MC JC | 3,750,593 | Δ1,199 bp | 100% | insH | insH | |
| RA | 3,824,280 | T→C | 100% | pseudogene (413/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,326 | T→C | 100% | pseudogene (459/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,362 | A→T | 100% | pseudogene (495/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,368 | G→A | 100% | pseudogene (501/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,374 | C→T | 100% | pseudogene (507/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,380 | 2 bp→AA | 100% | pseudogene (513‑514/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,410 | T→A | 100% | pseudogene (543/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,514 | T→C | 100% | pseudogene (647/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,524 | T→G | 100% | pseudogene (657/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,533:1 | +G | 100% | pseudogene (666/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| MC JC | 4,310,365 | Δ1,199 bp | 100% | insH–[alsK] | insH, [alsK] | |
| RA | 4,371,273 | Δ2 bp | 100% | intergenic (‑6/+299) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,563,589 | T→A | 100% | K207M (AAG→ATG) | iadA ← | isoaspartyl dipeptidase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | W3110S.gb | 379214 | 379279 | 66 | 7 [6] | [6] 7 | frmR/yaiO | regulator protein that represses frmRAB operon/hypothetical protein |
| * | * | ÷ | W3110S.gb | 422763 | 422790 | 28 | 8 [6] | [6] 7 | malZ | maltodextrin glucosidase |
| * | * | ÷ | W3110S.gb | 573851–575008 | 575999 | 992–2149 | 7 [6] | [0] 92 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 598760 | 598818 | 59 | 8 [6] | [5] 7 | cusA | copper/silver efflux system, membrane component |
| * | * | ÷ | W3110S.gb | 721518 | 721545 | 28 | 8 [6] | [6] 8 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 1421300 | 1421332 | 33 | 7 [3] | [6] 7 | ydaG/racR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 2569107 | 2569141 | 35 | 7 [4] | [5] 7 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 4213624–4216712 | 4216712 | 1–3089 | 8 [6] | [6] 8 | rrlE–[rrfE] | rrlE,[rrfE] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | = 20030 | NA (NA) | 3 (0.100) | 3/90 | NT | NA | coding (285/504 nt) | insB | IS1 transposase InsAB' |
| ? | W3110S.gb | = 20039 | NA (NA) | coding (276/504 nt) | insB | IS1 transposase InsAB' | |||||
| * | ? | W3110S.gb | 70061 = | 31 (0.930) | 24 (0.930) +CGCGTACAACT |
17/78 | NT | 41.3% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 57 (1.710) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 71265 | 34 (1.020) | 7 (0.290) +AGGGTCCCTAAGTC |
6/72 | NT | 28.6% | coding (879/879 nt) | araC | DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 3464879 = | 15 (0.450) | intergenic (‑255/+46) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA | |||||
| * | ? | W3110S.gb | 225408 = | NA (NA) | 5 (0.170) | 3/90 | NT | NA | noncoding (28/77 nt) | ileV | tRNA‑Ile |
| ? | W3110S.gb | 225425 = | NA (NA) | noncoding (45/77 nt) | ileV | tRNA‑Ile | |||||
| * | ? | W3110S.gb | = 225915 | NA (NA) | 3 (0.110) | 3/84 | NT | NA | noncoding (157/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | W3110S.gb | = 225926 | NA (NA) | noncoding (168/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | W3110S.gb | = 236798 | 26 (0.780) | 4 (0.120) | 4/98 | NT | 14.2% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | W3110S.gb | 2855720 = | 23 (0.700) | intergenic (‑258/‑29) | ygbA/mutS | hypothetical protein/methyl‑directed mismatch repair protein | |||||
| * | ? | W3110S.gb | 273327 = | NA (NA) | 5 (0.160) | 4/92 | NT | NA | coding (1015/1017 nt) | insH | IS5 transposase and trans‑activator |
| ? | W3110S.gb | 273345 = | NA (NA) | coding (997/1017 nt) | insH | IS5 transposase and trans‑activator | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 44 (1.320) | 26/100 | NT | 100% | intergenic (‑32/‑176) | insH/mmuP | IS5 transposase and trans‑activator/predicted S‑methylmethionine transporter |
| ? | W3110S.gb | 576000 = | 0 (0.000) | pseudogene (109/1128 nt) | nmpC | DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin | |||||
| * | ? | W3110S.gb | 314453 = | 26 (0.780) | 28 (0.870) +TC |
24/96 | NT | 69.2% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | 3932930 = | 0 (0.000) | coding (219/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 315707 | NA (NA) | 37 (1.110) | 31/100 | NT | 100% | coding (654/687 nt) | ykgA | predicted DNA‑binding transcriptional regulator |
| ? | W3110S.gb | 576911 = | 0 (0.000) | coding (76/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 566000 = | NA (NA) | 49 (1.470) | 31/100 | NT | 100% | intergenic (+90/‑56) | ybcD/insE | DLP12 prophage region; ECK0532:JW0527:b4508; predicted replication protein fragment/IS3 element protein InsE |
| ? | W3110S.gb | = 576913 | 0 (0.000) | coding (78/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 713380 = | 25 (0.750) | 10 (0.330) | 10/92 | NT | 31.3% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 21 (0.680) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 56 (1.680) | 24 (0.720) | 20/100 | NT | 34.0% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 37 (1.110) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | 1209367 = | 8 (0.240) | 14 (0.620) | 11/68 | NT | 71.1% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 6 (0.270) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1209382 | 7 (0.210) | 6 (0.270) | 6/68 | NT | 52.8% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | = 1211179 | 6 (0.270) | pseudogene (54/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | 2018571 = | 4 (0.120) | 21 (0.670) | 16/94 | NT | 84.8% | coding (567/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | 2519723 = | NA (NA) | intergenic (+33/‑54) | nupC/insL | nucleoside (except guanosine) transporter/predicted transposase | |||||
| * | ? | W3110S.gb | = 2018583 | 0 (0.000) | 23 (0.720) | 19/96 | NT | 100% | coding (579/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | = 2521059 | NA (NA) | intergenic (+170/+30) | insL/yfeA | predicted transposase/predicted diguanylate cyclase | |||||
| * | ? | W3110S.gb | 2172308 = | NA (NA) | 41 (1.250) | 33/98 | NT | 100% | pseudogene (1563/2041 nt) | gatR | DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 |
| ? | W3110S.gb | = 3920281 | 0 (0.000) | coding (88/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173564 | NA (NA) | 37 (1.130) | 29/98 | NT | 100% | pseudogene (307/2041 nt) pseudogene (307/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | 3920278 = | 0 (0.000) | coding (91/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173565 | NA (NA) | 32 (0.960) | 23/100 | NT | 100% | pseudogene (306/2041 nt) pseudogene (306/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | = 3932933 | 0 (0.000) | coding (222/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 2269762 | 20 (0.600) | 3 (0.100) | 3/92 | NT | 9.9% | coding (184/1467 nt) | yeiQ | predicted dehydrogenase, NAD‑dependent |
| ? | W3110S.gb | = 2269789 | 36 (1.170) | coding (211/1467 nt) | yeiQ | predicted dehydrogenase, NAD‑dependent | |||||
| * | ? | W3110S.gb | = 2412225 | NA (NA) | 41 (1.230) | 33/100 | NT | 95.3% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 2 (0.060) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | = 2540846 | 29 (0.870) | 3 (0.100) | 3/88 | NT | 9.8% | coding (1335/1728 nt) | ptsI | PEP‑protein phosphotransferase of PTS system |
| ? | W3110S.gb | = 2540852 | 30 (1.020) | coding (1341/1728 nt) | ptsI | PEP‑protein phosphotransferase of PTS system | |||||
| * | ? | W3110S.gb | 2724856 = | NA (NA) | 3 (0.100) | 3/88 | NT | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA/23S ribosomal RNA |
| ? | W3110S.gb | 2724880 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | W3110S.gb | = 2782231 | 42 (1.260) | 3 (0.090) | 3/96 | NT | 7.2% | intergenic (‑367/+63) | pinH/ypjB | ECK2645:JW5423:b2648; predicted invertase fragment/hypothetical protein |
| ? | W3110S.gb | = 2782248 | 37 (1.150) | intergenic (‑384/+46) | pinH/ypjB | ECK2645:JW5423:b2648; predicted invertase fragment/hypothetical protein | |||||
| * | ? | W3110S.gb | = 2855747 | 18 (0.540) | 10 (0.310) | 7/98 | NT | 25.8% | intergenic (‑285/‑2) | ygbA/mutS | hypothetical protein/methyl‑directed mismatch repair protein |
| ? | W3110S.gb | 4124505 = | 40 (1.220) | coding (1/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | 3690778 = | NA (NA) | 4 (0.120) | 3/98 | NT | NA | noncoding (2202/2904 nt) | rrlC | 23S ribosomal RNA |
| ? | W3110S.gb | 3690797 = | NA (NA) | noncoding (2183/2904 nt) | rrlC | 23S ribosomal RNA | |||||
| * | ? | W3110S.gb | = 3698308 | 33 (0.990) | 3 (0.110) | 3/82 | NT | 10.0% | coding (149/993 nt) | rbsR | DNA‑binding transcriptional repressor |
| ? | W3110S.gb | = 3698315 | 27 (0.990) | coding (142/993 nt) | rbsR | DNA‑binding transcriptional repressor | |||||
| * | ? | W3110S.gb | 3748799 = | 2 (0.060) | 34 (1.020) | 26/100 | NT | 94.4% | coding (184/984 nt) | tnaB | tryptophan transporter of low affinity |
| ? | W3110S.gb | 4056222 = | NA (NA) | intergenic (‑564/+15) | yrhB/insB | hypothetical protein/IS1 transposase InsAB' | |||||
| * | ? | W3110S.gb | 3986482 = | 25 (0.750) | 3 (0.100) | 3/90 | NT | 11.0% | intergenic (‑26/‑737) | slp/insH | outer membrane lipoprotein/IS5 transposase and trans‑activator |
| ? | W3110S.gb | 3986513 = | 26 (0.870) | intergenic (‑57/‑706) | slp/insH | outer membrane lipoprotein/IS5 transposase and trans‑activator | |||||
| * | ? | W3110S.gb | 4547364 = | 23 (0.690) | 4 (0.150) | 4/82 | NT | 20.1% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 13 (0.480) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||
| * | ? | W3110S.gb | = 4547372 | 16 (0.480) | 7 (0.260) | 7/82 | NT | 34.9% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | = 4547668 | 13 (0.480) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||