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 | annotation | gene | description |
| RA | 156,056 | T→G | N49T (AAT→ACT) | Y75_RS00710 ← | fimbrial chaperone |
| RA | 547,694 | A→G | E38E (GAA→GAG) | Y75_RS02655 → | hypothetical protein |
| RA | 547,835 | +G | coding (255/261 nt) | Y75_RS02655 → | hypothetical protein |
| RA | 556,858 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD |
| MC JC | 654,214 | Δ1,199 bp | Y75_RS03225–[dcuC] | Y75_RS03225, [dcuC] | |
| RA | 666,783 | A→T | D619E (GAT→GAA) | mrdA ← | peptidoglycan DD‑transpeptidase MrdA |
| RA | 987,574 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | porin OmpF/asparagine‑‑tRNA ligase |
| RA | 1,093,686 | T→C | V130A (GTA→GCA) | Y75_RS05355 → | GGDEF domain‑containing protein |
| RA | 1,197,797 | C→T | H366H (CAC→CAT) | icd → | NADP‑dependent isocitrate dehydrogenase |
| RA | 1,197,809 | C→T | T370T (ACC→ACT) | icd → | NADP‑dependent isocitrate dehydrogenase |
| RA | 1,197,822 | T→C | L375M (TTA→CTG) | icd → | NADP‑dependent isocitrate dehydrogenase |
| RA | 1,197,824 | A→G | L375M (TTA→CTG) | icd → | NADP‑dependent isocitrate dehydrogenase |
| MC JC | 1,301,041 | Δ1,336 bp | Y75_RS06530–Y75_RS06530 | Y75_RS06530, Y75_RS06530 | |
| RA | 1,459,205 | G→A | G354G (GGG→GGA) | paaK → | phenylacetate‑CoA oxygenase/reductase subunit PaaK |
| RA | 1,519,222 | G→T | V40V (GTG→GTT) | Y75_RS07640 → | orphan toxin OrtT |
| RA | 1,669,601 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,979,957 | G→T | intergenic (‑46/+398) | flhD ← / ← Y75_RS09980 | flagellar transcriptional regulator FlhD/IS5‑like element IS5 family transposase |
| RA | 2,005,401 | C→T | E115K (GAA→AAA) | fliC ← | H48 family flagellin FliC |
| MC JC | 2,176,983 | Δ1,199 bp | Y75_RS10980–[gatA] | Y75_RS10980, [gatA] | |
| RA | 2,245,455 | A→G | S283P (TCG→CCG) | Y75_RS11290 ← | DUF418 family protein |
| MC JC | 2,320,795 | Δ1,336 bp | Y75_RS11650–[rcsC] | Y75_RS11650, Y75_RS11650, [rcsC] | |
| RA | 2,739,952 | C→A | intergenic (‑146/‑64) | aroF ← / → Y75_RS13630 | 3‑deoxy‑7‑phosphoheptulonate synthase AroF/DUF2799 domain‑containing protein |
| RA | 2,865,825 | A→T | pseudogene (383/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,866,111 | A→G | pseudogene (97/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,169,126 | A→C | T215P (ACA→CCA) | qseB → | two‑component system response regulator QseB |
| RA | 3,268,825 | A→G | T186A (ACA→GCA) | Y75_RS16240 → | YhaC family protein |
| MC JC | 3,742,936 | Δ1,336 bp | Y75_RS18560–Y75_RS18560 | Y75_RS18560, Y75_RS18560 | |
| MC JC | 3,746,911 | Δ1,199 bp | Y75_RS18585–[tnaB] | Y75_RS18585, [tnaB] | |
| MC JC | 3,958,123 | Δ34 bp | coding (1156‑1189/1287 nt) | Y75_RS19595 → | C4‑dicarboxylate transporter DctC |
| RA | 3,975,201 | G→T | L199F (TTG→TTT) | gadX → | acid resistance transcriptional activator GadX |
| MC JC | 4,310,363 | Δ1,199 bp | Y75_RS21310–[alsK] | Y75_RS21310, [alsK] | |
| RA | 4,371,274 | (A)5→3 | pseudogene (179‑180/1304 nt) | Y75_RS21600 ← | anaerobic C4‑dicarboxylate transporter |
| RA | 4,626,165 | C→G | C201W (TGC→TGG) | deoD → | purine‑nucleoside phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_007779 | 1197834 | 1213126 | 15293 | 92 [90] | [90] 91 | [icd]–[Y75_RS23470] | [icd],Y75_RS05945,Y75_RS05950,lit,Y75_RS05960,Y75_RS05965,Y75_RS24820,Y75_RS23460,Y75_RS05970,Y75_RS05975,Y75_RS05980,ymfL,Y75_RS23465,Y75_RS05995,Y75_RS06000,Y75_RS06005,Y75_RS06010,Y75_RS06015,Y75_RS06020,Y75_RS06025,Y75_RS06030,Y75_RS06035,pinE,Y75_RS06045,[Y75_RS23470] |
| * | * | ÷ | NC_007779 | 2068445–2069342 | 2069342 | 1–898 | 92 [90] | [90] 92 | Y75_RS10470 | IS5‑like element IS5 family transposase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | = 20563 | NA (NA) | 165 (1.070) | 140/496 | 0.1 | 98.8% | intergenic (‑55/+252) | Y75_RS00100/rpsT | IS1‑like element IS1A family transposase/30S ribosomal protein S20 |
| ? | NC_007779 | 755210 = | 2 (0.010) | intergenic (‑7/‑374) | Y75_RS24790/sdhC | hypothetical protein/succinate dehydrogenase cytochrome b556 subunit | |||||
| * | ? | NC_007779 | 289857 = | 154 (1.000) | 203 (1.330) | 166/492 | 0.0 | 71.8% | intergenic (+1/+16) | Y75_RS23110/Y75_RS01415 | DUF3987 domain‑containing protein/IS1 family transposase |
| ? | NC_007779 | = 755217 | 7 (0.050) | intergenic (‑14/‑367) | Y75_RS24790/sdhC | hypothetical protein/succinate dehydrogenase cytochrome b556 subunit | |||||
| * | ? | NC_007779 | 380484 = | NA (NA) | 135 (0.880) | 124/496 | 0.4 | NA | coding (28/444 nt) | Y75_RS01845 | transferase |
| ? | NC_007779 | = 381407 | NA (NA) | coding (518/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase | |||||
| * | ? | NC_007779 | 2810717 = | 3 (0.020) | 157 (1.020) | 134/496 | 0.2 | 98.1% | coding (635/1173 nt) | emrA | multidrug efflux MFS transporter periplasmic adaptor subunit EmrA |
| ? | NC_007779 | 2995017 = | NA (NA) | intergenic (‑1/+11) | Y75_RS24115/Y75_RS14910 | type III secretion apparatus protein OrgA/MxiK/IS3‑like element IS2 family transposase | |||||
| * | ? | NC_007779 | = 2810721 | 3 (0.020) | 179 (1.160) | 146/496 | 0.1 | 98.4% | coding (639/1173 nt) | emrA | multidrug efflux MFS transporter periplasmic adaptor subunit EmrA |
| ? | NC_007779 | = 2996347 | NA (NA) | pseudogene (1138/1140 nt) | Y75_RS14925 | hypothetical protein | |||||
| * | ? | NC_007779 | 3128802 = | NA (NA) | 172 (1.120) | 129/496 | 0.3 | 98.3% | coding (34/1137 nt) | Y75_RS15525 | hypothetical protein |
| ? | NC_007779 | = 3189141 | 3 (0.020) | coding (605/750 nt) | Y75_RS15855 | molecular chaperone | |||||
| * | ? | NC_007779 | = 3129996 | NA (NA) | 170 (1.100) | 132/496 | 0.2 | 96.0% | intergenic (+146/+1) | Y75_RS15530/Y75_RS15535 | IS5‑like element IS5 family transposase/lipopolysaccharide biosynthesis protein |
| ? | NC_007779 | 3189138 = | 7 (0.050) | coding (602/750 nt) | Y75_RS15855 | molecular chaperone | |||||
| * | ? | NC_007779 | = 3186081 | NA (NA) | 173 (1.130) | 137/494 | 0.1 | 96.1% | coding (26/2466 nt) | Y75_RS15850 | fimbrial biogenesis outer membrane usher protein |
| ? | NC_007779 | 3512753 = | 7 (0.050) | coding (529/1026 nt) | cytR | DNA‑binding transcriptional regulator CytR | |||||
| * | ? | NC_007779 | 3188360 = | 6 (0.040) | 195 (1.270) | 123/496 | 0.4 | 97.0% | coding (2305/2466 nt) | Y75_RS15850 | fimbrial biogenesis outer membrane usher protein |
| ? | NC_007779 | 3746911 = | NA (NA) | intergenic (‑3/‑32) | Y75_RS18580/Y75_RS18585 | tryptophan permease/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 3188364 | 3 (0.020) | 228 (1.490) | 155/494 | 0.0 | 98.7% | coding (2309/2466 nt) | Y75_RS15850 | fimbrial biogenesis outer membrane usher protein |
| ? | NC_007779 | = 3262327 | NA (NA) | intergenic (+145/+4) | Y75_RS16205/tdcD | IS5‑like element IS5 family transposase/propionate kinase | |||||
| * | ? | NC_007779 | = 3261133 | 0 (0.000) | 179 (1.180) | 137/488 | 0.1 | 100% | intergenic (‑59/‑33) | tdcE/Y75_RS16205 | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 3262333 = | 0 (0.000) | pseudogene (1183/1185 nt) | tdcD | propionate kinase | |||||
| * | ? | NC_007779 | = 3512759 | 2 (0.010) | 191 (1.250) | 140/494 | 0.1 | 99.0% | coding (535/1026 nt) | cytR | DNA‑binding transcriptional regulator CytR |
| ? | NC_007779 | = 3744262 | NA (NA) | intergenic (‑45/+31) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ | |||||
| * | ? | NC_007779 | = 3744263 | NA (NA) | 147 (0.950) | 127/496 | 0.3 | 99.3% | intergenic (‑46/+30) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ |
| ? | NC_007779 | 3903274 = | 1 (0.010) | coding (37/825 nt) | Y75_RS19350 | protein bax | |||||
| * | ? | NC_007779 | = 3750590 | 0 (0.000) | 162 (1.070) | 142/488 | 0.1 | 100% | intergenic (‑104/‑33) | tnaA/Y75_RS18600 | tryptophanase/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 3751790 = | 0 (0.000) | intergenic (+151/+116) | Y75_RS18600/tnaC | IS5‑like element IS5 family transposase/tryptophanase leader peptide | |||||
| * | ? | NC_007779 | = 3903279 | 3 (0.020) | 184 (1.200) | 151/494 | 0.0 | 98.4% | coding (42/825 nt) | Y75_RS19350 | protein bax |
| ? | NC_007779 | = 4504190 | NA (NA) | intergenic (+10/+167) | Y75_RS22280/Y75_RS22285 | IS3‑like element IS2 family transposase/phosphoethanolamine transferase | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 136 (0.880) | 113/496 | 0.7 | 97.8% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 4546700 = | 3 (0.020) | intergenic (+461/‑17) | fimB/fimE | type 1 fimbria regulatory protein FimB/type 1 fimbria regulatory protein FimE | |||||
| * | ? | NC_007779 | = 4311556 | NA (NA) | 127 (0.830) | 113/494 | 0.7 | 92.1% | intergenic (+145/+1) | Y75_RS21310/alsK | IS5‑like element IS5 family transposase/allose kinase |
| ? | NC_007779 | 4540915 = | 11 (0.070) | intergenic (+204/+379) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | = 4311556 | NA (NA) | 164 (1.070) | 130/494 | 0.2 | 98.2% | intergenic (+145/+1) | Y75_RS21310/alsK | IS5‑like element IS5 family transposase/allose kinase |
| ? | NC_007779 | = 4546704 | 3 (0.020) | intergenic (+465/‑13) | fimB/fimE | type 1 fimbria regulatory protein FimB/type 1 fimbria regulatory protein FimE | |||||
| * | ? | NC_007779 | 4547362 = | 56 (0.360) | 121 (0.820) | 107/478 | 0.8 | 68.4% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 58 (0.390) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 4547370 | 56 (0.360) | 117 (0.790) | 103/478 | 0.9 | 67.6% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 58 (0.390) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||