mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 105,411 | G→A | G36D (GGT→GAT) | ftsZ → | cell division protein FtsZ |
| RA | 444,525 | T→G | intergenic (+127/+1) | yajQ → / ← Y75_RS02195 | nucleotide binding protein YajQ/MFS transporter |
| RA | 490,998 | Δ1 bp | coding (363/552 nt) | apt → | adenine phosphoribosyltransferase |
| RA | 520,989 | G→T | P450P (CCG→CCT) | Y75_RS02550 → | ABC transporter permease |
| 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 | 556,778 | A→C | F63V (TTC→GTC) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD |
| 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 | 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 |
| MC JC | 1,301,041 | Δ1,336 bp | Y75_RS06530–Y75_RS06530 | Y75_RS06530, Y75_RS06530 | |
| RA | 1,519,222 | G→T | V40V (GTG→GTT) | Y75_RS07640 → | orphan toxin OrtT |
| RA | 1,565,001 | A→G | intergenic (‑211/+47) | ddpX ← / ← dosP | D‑alanyl‑D‑alanine dipeptidase/oxygen‑sensing cyclic‑di‑GMP phosphodiesterase |
| RA | 1,669,601 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,882,210 | G→A | L88L (CTC→CTT) | leuE ← | leucine efflux protein LeuE |
| RA | 1,932,183 | Δ1 bp | coding (279/291 nt) | yebG ← | DNA damage‑inducible protein YebG |
| 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 | 2,434,645 | A→T | V347E (GTG→GAG) | purF ← | amidophosphoribosyltransferase |
| RA | 2,866,111 | A→G | pseudogene (97/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| MC JC | 3,261,134 | Δ1,199 bp | Y75_RS16205–[tdcD] | Y75_RS16205, [tdcD] | |
| RA | 3,268,825 | A→G | T186A (ACA→GCA) | Y75_RS16240 → | YhaC family protein |
| JC | 3,277,128 | (TTCAACA)2→3 | coding (272/336 nt) | prlF → | type II toxin‑antitoxin system antitoxin PrlF |
| 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 |
| 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_007779 | 1197780 | 1213137 | 15358 | 134 [133] | [131] 134 | [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 | 3974162 | 3988254–3987179 | 13018–14093 | 176 [0] | [133] 134 | [Y75_RS19655]–Y75_RS19725 | [Y75_RS19655],gadX,gadW,Y75_RS19670,mdtE,Y75_RS19680,gadE,hdeD,hdeA,hdeB,Y75_RS19705,Y75_RS19710,slp,Y75_RS19720,Y75_RS19725 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 273179 = | NA (NA) | 214 (1.010) | 169/496 | 0.2 | 99.1% | intergenic (+2/+146) | Y75_RS01330/Y75_RS01335 | hypothetical protein/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 1106950 = | 2 (0.010) | intergenic (‑44/‑41) | Y75_RS05455/Y75_RS05465 | IS3‑like element IS2 family transposase/hypothetical protein | |||||
| * | ? | NC_007779 | = 274373 | NA (NA) | 234 (1.100) | 184/496 | 0.1 | 99.6% | intergenic (‑32/‑176) | Y75_RS01335/mmuP | IS5‑like element IS5 family transposase/S‑methylmethionine permease |
| ? | NC_007779 | = 380548 | 1 (0.000) | coding (19/361 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase | |||||
| * | ? | NC_007779 | 380484 = | NA (NA) | 194 (0.910) | 155/496 | 0.5 | 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 | = 2072408 | NA (NA) | 177 (0.840) | 144/492 | 0.9 | NA | intergenic (‑46/‑3) | Y75_RS10480/Y75_RS10490 | IS3‑like element IS2 family transposase/TonB‑dependent receptor plug domain‑containing protein |
| ? | NC_007779 | = 2105081 | NA (NA) | intergenic (‑33/+2) | Y75_RS10660/Y75_RS10665 | IS5‑like element IS5 family transposase/glycosyltransferase | |||||
| * | ? | NC_007779 | 2292253 = | NA (NA) | 226 (1.060) | 174/496 | 0.2 | 97.4% | pseudogene (3/2532 nt) | yejO | autotransporter YejO |
| ? | NC_007779 | = 2487193 | 6 (0.030) | coding (430/1539 nt) | emrY | multidrug efflux MFS transporter permease subunit EmrY | |||||
| * | ? | NC_007779 | = 2293447 | NA (NA) | 147 (0.690) | 120/496 | 2.3 | 95.5% | intergenic (‑32/‑387) | Y75_RS11495/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP |
| ? | NC_007779 | 2487190 = | 7 (0.030) | coding (433/1539 nt) | emrY | multidrug efflux MFS transporter permease subunit EmrY | |||||
| * | ? | NC_007779 | = 3186081 | NA (NA) | 226 (1.070) | 183/494 | 0.1 | 98.7% | coding (26/2466 nt) | Y75_RS15850 | fimbrial biogenesis outer membrane usher protein |
| ? | NC_007779 | 3512753 = | 3 (0.010) | coding (529/1026 nt) | cytR | DNA‑binding transcriptional regulator CytR | |||||
| * | ? | NC_007779 | = 3512759 | 5 (0.020) | 255 (1.200) | 180/494 | 0.1 | 98.1% | 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 | = 3744202 | NA (NA) | 220 (1.040) | 173/496 | 0.2 | NA | coding (16/361 nt) | Y75_RS18560 | IS3‑like element IS2 family transposase |
| ? | NC_007779 | = 3748105 | NA (NA) | intergenic (+146/+3) | Y75_RS18585/tnaB | IS5‑like element IS5 family transposase/low affinity tryptophan permease TnaB | |||||
| * | ? | NC_007779 | = 3744263 | NA (NA) | 194 (0.910) | 159/496 | 0.4 | 99.0% | intergenic (‑46/+30) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ |
| ? | NC_007779 | 3903274 = | 2 (0.010) | coding (37/825 nt) | Y75_RS19350 | protein bax | |||||
| * | ? | NC_007779 | 3746912 = | NA (NA) | 176 (0.830) | 141/494 | 1.0 | 100% | intergenic (‑4/‑31) | Y75_RS18580/Y75_RS18585 | tryptophan permease/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 3974161 | 0 (0.000) | coding (1327/1401 nt) | Y75_RS19655 | glutamate decarboxylase | |||||
| * | ? | NC_007779 | = 3750590 | 0 (0.000) | 263 (1.260) | 192/488 | 0.0 | 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 | 4 (0.020) | 255 (1.200) | 191/494 | 0.0 | 98.5% | 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 | = 3988377 | NA (NA) | 214 (1.020) | 164/492 | 0.3 | 99.5% | coding (748/783 nt) | Y75_RS19730 | hypothetical protein |
| ? | NC_007779 | = 4547133 | 1 (0.000) | coding (417/597 nt) | fimE | type 1 fimbria regulatory protein FimE | |||||
| * | ? | NC_007779 | = 3988379 | NA (NA) | 271 (1.270) | 188/496 | 0.0 | 98.6% | coding (746/783 nt) | Y75_RS19730 | hypothetical protein |
| ? | NC_007779 | 4495464 = | 4 (0.020) | coding (356/999 nt) | idnR | DNA‑binding transcriptional regulator IdnR | |||||
| * | ? | NC_007779 | 4218985 = | 2 (0.010) | 304 (1.440) | 184/494 | 0.1 | 99.4% | intergenic (+186/‑83) | metA/aceB | homoserine O‑succinyltransferase/malate synthase A |
| ? | NC_007779 | 4310364 = | NA (NA) | intergenic (‑288/‑31) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 4218989 | 7 (0.030) | 314 (1.480) | 183/496 | 0.1 | 97.8% | intergenic (+190/‑79) | metA/aceB | homoserine O‑succinyltransferase/malate synthase A |
| ? | NC_007779 | = 4311557 | NA (NA) | pseudogene (921/921 nt) | alsK | allose kinase | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 256 (1.200) | 189/496 | 0.0 | 96.6% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4495467 | 9 (0.040) | coding (353/999 nt) | idnR | DNA‑binding transcriptional regulator IdnR | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 195 (0.920) | 155/496 | 0.5 | 96.5% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 4547128 = | 7 (0.030) | coding (412/597 nt) | fimE | type 1 fimbria regulatory protein FimE | |||||
| * | ? | NC_007779 | = 4311556 | NA (NA) | 193 (0.910) | 154/494 | 0.5 | 96.0% | intergenic (+145/+1) | Y75_RS21310/alsK | IS5‑like element IS5 family transposase/allose kinase |
| ? | NC_007779 | 4540915 = | 8 (0.040) | intergenic (+204/+379) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | 4547362 = | 55 (0.260) | 170 (0.830) | 141/478 | 0.8 | 74.4% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 64 (0.310) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 4547370 | 55 (0.260) | 173 (0.840) | 145/478 | 0.7 | 74.7% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 64 (0.310) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||