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 | 56,273 | G→A | L279L (CTC→CTT) | lptD ← | LPS assembly protein LptD |
| 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 |
| 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 |
| RA | 1,213,665 | (C)8→9 | intergenic (‑85/+452) | iraM ← / ← Y75_RS24825 | anti‑adapter protein IraM/hypothetical 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 | 1,669,601 | 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 | 2,646,569 | C→A | E1459* (GAG→TAG) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,866,111 | A→G | pseudogene (97/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,931,775 | C→A | P190P (CCG→CCT) | fucA ← | L‑fuculose‑phosphate aldolase |
| 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 |
| RA | 3,454,320 | C→T | G373S (GGC→AGC) | rpoB ← | DNA‑directed RNA polymerase subunit beta |
| RA | 3,532,025 | A→G | N107S (AAC→AGC) | cpxA → | envelope stress sensor histidine kinase CpxA |
| 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 | 3,750,591 | Δ1,199 bp | Y75_RS18600 | Y75_RS18600 | |
| RA | 3,948,766 | G→A | R320H (CGT→CAT) | bcsB → | cellulose biosynthesis cyclic di‑GMP‑binding regulatory protein BcsB |
| MC JC | 3,958,123 | Δ34 bp | coding (1156‑1189/1287 nt) | Y75_RS19595 → | C4‑dicarboxylate transporter DctC |
| RA | 4,200,197 | A→C | K271Q (AAA→CAA) | rpoA → | DNA‑directed RNA polymerase subunit alpha |
| 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 | 1197833 | 1213073 | 15241 | 53 [52] | [49] 54 | [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 | 3976435 | 3988253–3987179 | 10745–11819 | 94 [0] | [52] 54 | [gadW]–Y75_RS19725 | [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 | = 274373 | NA (NA) | 109 (1.100) | 87/498 | 0.3 | 100% | intergenic (‑32/‑176) | Y75_RS01335/mmuP | IS5‑like element IS5 family transposase/S‑methylmethionine permease |
| ? | NC_007779 | 1218024 = | 0 (0.000) | coding (79/267 nt) | ariR | biofilm/acid‑resistance regulator AriR | |||||
| * | ? | NC_007779 | 380484 = | NA (NA) | 87 (0.880) | 76/498 | 0.6 | 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 | 381401 = | NA (NA) | 81 (0.830) | 69/494 | 0.9 | NA | coding (512/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase |
| ? | NC_007779 | = 381812 | NA (NA) | pseudogene (174/174 nt) | Y75_RS23175 | acetyltransferase | |||||
| * | ? | NC_007779 | = 1218027 | 1 (0.010) | 117 (1.190) | 91/498 | 0.2 | 99.2% | coding (82/267 nt) | ariR | biofilm/acid‑resistance regulator AriR |
| ? | NC_007779 | 1980209 = | NA (NA) | intergenic (‑298/+146) | flhD/Y75_RS09980 | flagellar transcriptional regulator FlhD/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | 1349606 = | 2 (0.020) | 93 (0.940) | 80/498 | 0.5 | 97.9% | coding (1021/1935 nt) | rnb | exoribonuclease II |
| ? | NC_007779 | 1980209 = | NA (NA) | intergenic (‑298/+146) | flhD/Y75_RS09980 | flagellar transcriptional regulator FlhD/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 1349609 | 2 (0.020) | 113 (1.150) | 93/498 | 0.2 | 98.3% | coding (1018/1935 nt) | rnb | exoribonuclease II |
| ? | NC_007779 | 1397758 = | NA (NA) | intergenic (‑122/‑32) | ynaI/Y75_RS07025 | low conductance mechanosensitive channel YnaI/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 3186081 | NA (NA) | 99 (1.010) | 88/496 | 0.2 | 97.1% | coding (26/2466 nt) | Y75_RS15850 | fimbrial biogenesis outer membrane usher protein |
| ? | NC_007779 | 3512753 = | 3 (0.030) | coding (529/1026 nt) | cytR | DNA‑binding transcriptional regulator CytR | |||||
| * | ? | NC_007779 | = 3512759 | 5 (0.050) | 97 (0.990) | 82/496 | 0.4 | 95.1% | 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 | = 3744263 | NA (NA) | 99 (1.000) | 85/498 | 0.3 | 98.0% | intergenic (‑46/+30) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ |
| ? | NC_007779 | 3903274 = | 2 (0.020) | coding (37/825 nt) | Y75_RS19350 | protein bax | |||||
| * | ? | NC_007779 | = 3903279 | 2 (0.020) | 100 (1.020) | 89/496 | 0.2 | 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 | = 3976434 | 0 (0.000) | 93 (0.940) | 79/498 | 0.5 | 100% | coding (638/729 nt) | gadW | acid resistance transcriptional activator GadW |
| ? | NC_007779 | 3987185 = | NA (NA) | pseudogene (3/379 nt) | Y75_RS19720 | hypothetical protein | |||||
| * | ? | NC_007779 | = 4311556 | NA (NA) | 88 (0.900) | 79/496 | 0.5 | 94.6% | intergenic (+145/+1) | Y75_RS21310/alsK | IS5‑like element IS5 family transposase/allose kinase |
| ? | NC_007779 | 4540915 = | 5 (0.050) | intergenic (+204/+379) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||