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 | 62,682 | +G | coding (583/2907 nt) | rapA ← | RNA polymerase‑associated protein RapA |
| RA | 277,827 | C→G | G67A (GGC→GCC) | Y75_RS01350 ← | ferric ABC transporter ATP‑binding protein |
| MC JC | 490,544 | Δ6 bp | intergenic (+61/‑87) | Y75_RS02410 → / → apt | DUF454 family protein/adenine phosphoribosyltransferase |
| 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 |
| RA | 573,671 | T→A | intergenic (+109/+289) | quuD → / ← Y75_RS02845 | antitermination protein QuuD/IS5‑like element IS5 family transposase |
| 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 |
| RA | 1,197,797 | C→T | H366H (CAC→CAT) | icd → | NADP‑dependent isocitrate dehydrogenase |
| 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 |
| MC JC | 1,618,943 | Δ6,115 bp | [ydeA]–[dgcZ] | [ydeA], marC, marR, marA, marB, eamA, ydeE, mgtS, [dgcZ] | |
| 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 |
| RA | 2,093,073 | G→A | E249K (GAA→AAA) | hisG → | ATP phosphoribosyltransferase |
| 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 | 2,866,111 | A→G | pseudogene (97/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,241,721 | G→T | L84M (CTG→ATG) | Y75_RS16095 ← | altronate dehydratase |
| 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 |
| 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 | 4,297,865 | +T | intergenic (+136/‑206) | nrfG → / → gltP | heme lyase NrfEFG subunit NrfG/glutamate/aspartate:proton symporter GltP |
| 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 | 4,547,650 | Δ1 bp | intergenic (+337/‑145) | fimE → / → fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_007779 | 1197804 | 1213113 | 15310 | 92 [90] | [91] 92 | [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 | 3987267–3988384 | 3988834 | 451–1568 | 92 [91] | [1] 130 | [Y75_RS19725]–[Y75_RS19730] | [Y75_RS19725],[Y75_RS19730] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 89166 = | 3 (0.020) | 151 (0.980) | 116/496 | 0.6 | 98.0% | intergenic (+134/‑468) | cra/mraZ | catabolite repressor/activator/division/cell wall cluster transcriptional repressor MraZ |
| ? | NC_007779 | = 274373 | NA (NA) | intergenic (‑32/‑176) | Y75_RS01335/mmuP | IS5‑like element IS5 family transposase/S‑methylmethionine permease | |||||
| * | ? | NC_007779 | = 89169 | 1 (0.010) | 153 (1.000) | 120/496 | 0.4 | 99.4% | intergenic (+137/‑465) | cra/mraZ | catabolite repressor/activator/division/cell wall cluster transcriptional repressor MraZ |
| ? | NC_007779 | 273179 = | NA (NA) | intergenic (+2/+146) | Y75_RS01330/Y75_RS01335 | hypothetical protein/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | 380484 = | NA (NA) | 126 (0.820) | 105/496 | 1.0 | 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 | 1397758 = | NA (NA) | 147 (0.960) | 125/496 | 0.3 | 99.3% | intergenic (‑122/‑32) | ynaI/Y75_RS07025 | low conductance mechanosensitive channel YnaI/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 1549542 = | 1 (0.010) | coding (428/3048 nt) | fdnG | formate dehydrogenase‑N subunit alpha | |||||
| * | ? | NC_007779 | = 1398952 | NA (NA) | 170 (1.110) | 125/496 | 0.3 | 97.7% | intergenic (+146/‑127) | Y75_RS07025/Y75_RS07030 | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NC_007779 | = 1549545 | 4 (0.030) | coding (431/3048 nt) | fdnG | formate dehydrogenase‑N subunit alpha | |||||
| * | ? | NC_007779 | 1822768 = | 5 (0.030) | 179 (1.170) | 128/494 | 0.2 | 97.3% | coding (161/1359 nt) | chbC | PTS N,N'‑diacetylchitobiose transporter subunit IIC |
| ? | NC_007779 | 2176984 = | NA (NA) | intergenic (‑4/‑31) | gatA/Y75_RS10980 | PTS galactitol transporter subunit IIA/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 1822772 | 4 (0.030) | 164 (1.070) | 121/496 | 0.4 | 97.6% | coding (157/1359 nt) | chbC | PTS N,N'‑diacetylchitobiose transporter subunit IIC |
| ? | NC_007779 | 1980209 = | NA (NA) | intergenic (‑298/+146) | flhD/Y75_RS09980 | flagellar transcriptional regulator FlhD/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 3186081 | NA (NA) | 175 (1.140) | 131/494 | 0.2 | 97.2% | coding (26/2466 nt) | Y75_RS15850 | fimbrial biogenesis outer membrane usher protein |
| ? | NC_007779 | 3512753 = | 5 (0.030) | coding (529/1026 nt) | cytR | DNA‑binding transcriptional regulator CytR | |||||
| * | ? | NC_007779 | 3277113 = | 10 (0.070) | 166 (1.100) +TTGAA |
140/486 | 0.1 | 94.4% | coding (257/336 nt) | prlF | type II toxin‑antitoxin system antitoxin PrlF |
| ? | NC_007779 | = 3277128 | NA (NA) | coding (272/336 nt) | prlF | type II toxin‑antitoxin system antitoxin PrlF | |||||
| * | ? | NC_007779 | = 3512759 | 1 (0.010) | 143 (0.940) | 115/494 | 0.6 | 99.3% | 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) | 158 (1.030) | 134/496 | 0.2 | 98.1% | intergenic (‑46/+30) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ |
| ? | NC_007779 | 3903274 = | 3 (0.020) | coding (37/825 nt) | Y75_RS19350 | protein bax | |||||
| * | ? | NC_007779 | 3746912 = | NA (NA) | 158 (1.030) | 124/494 | 0.3 | 97.5% | intergenic (‑4/‑31) | Y75_RS18580/Y75_RS18585 | tryptophan permease/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 3975234 | 4 (0.030) | coding (630/825 nt) | gadX | acid resistance transcriptional activator GadX | |||||
| * | ? | NC_007779 | = 3750590 | 0 (0.000) | 127 (0.840) | 110/488 | 0.7 | 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) | 150 (0.980) | 125/494 | 0.3 | 98.0% | 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 | 3975230 = | 2 (0.010) | 179 (1.170) | 132/496 | 0.2 | 98.9% | coding (626/825 nt) | gadX | acid resistance transcriptional activator GadX |
| ? | NC_007779 | = 3988379 | NA (NA) | coding (746/783 nt) | Y75_RS19730 | hypothetical protein | |||||
| * | ? | NC_007779 | = 3988379 | NA (NA) | 129 (0.840) | 108/496 | 0.9 | 99.2% | coding (746/783 nt) | Y75_RS19730 | hypothetical protein |
| ? | NC_007779 | 3988835 = | 1 (0.010) | coding (290/783 nt) | Y75_RS19730 | hypothetical protein | |||||
| * | ? | NC_007779 | = 4311556 | NA (NA) | 127 (0.830) | 109/494 | 0.8 | 97.0% | intergenic (+145/+1) | Y75_RS21310/alsK | IS5‑like element IS5 family transposase/allose kinase |
| ? | NC_007779 | 4540915 = | 4 (0.030) | intergenic (+204/+379) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||