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 | 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 | 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 |
| 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 | 2,866,111 | 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 |
| RA | 3,532,022 | G→T | R106L (CGT→CTT) | 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 | |
| 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 | 1197822 | 1213088 | 15267 | 77 [72] | [75] 77 | [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 | 3982164 | 8003 | 129 [0] | [2] 123 | [Y75_RS19655]–gadE | [Y75_RS19655],gadX,gadW,Y75_RS19670,mdtE,Y75_RS19680,gadE |
| * | * | ÷ | NC_007779 | 3987318–3988377 | 3989658 | 1282–2341 | 76 [75] | [1] 147 | [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 | 273179 = | NA (NA) | 116 (0.860) | 106/496 | 0.5 | 99.2% | intergenic (+2/+146) | Y75_RS01330/Y75_RS01335 | hypothetical protein/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 1106950 = | 1 (0.010) | intergenic (‑44/‑41) | Y75_RS05455/Y75_RS05465 | IS3‑like element IS2 family transposase/hypothetical protein | |||||
| * | ? | NC_007779 | 380484 = | NA (NA) | 124 (0.920) | 109/496 | 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 | 381401 = | NA (NA) | 76 (0.570) | 66/492 | 3.0 | 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 | 1215890 = | 1 (0.010) | 123 (0.910) | 98/496 | 0.7 | 99.2% | coding (1163/1212 nt) | bluF | blue light‑responsive regulator BluF |
| ? | NC_007779 | = 1398952 | NA (NA) | intergenic (+146/‑127) | Y75_RS07025/Y75_RS07030 | IS5‑like element IS5 family transposase/DUF2534 family protein | |||||
| * | ? | NC_007779 | = 1215893 | 2 (0.010) | 157 (1.160) | 121/496 | 0.1 | 98.7% | coding (1160/1212 nt) | bluF | blue light‑responsive regulator BluF |
| ? | NC_007779 | 1397758 = | NA (NA) | intergenic (‑122/‑32) | ynaI/Y75_RS07025 | low conductance mechanosensitive channel YnaI/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 1398952 | NA (NA) | 119 (0.880) | 105/496 | 0.5 | 97.5% | intergenic (+146/‑127) | Y75_RS07025/Y75_RS07030 | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NC_007779 | = 1772685 | 3 (0.020) | coding (357/357 nt) | Y75_RS08895 | YdiL family protein | |||||
| * | ? | NC_007779 | 1772682 = | 3 (0.020) | 136 (1.000) | 114/496 | 0.3 | 97.8% | coding (354/357 nt) | Y75_RS08895 | YdiL family protein |
| ? | NC_007779 | 2176983 = | NA (NA) | intergenic (‑3/‑32) | gatA/Y75_RS10980 | PTS galactitol transporter subunit IIA/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 2072408 | NA (NA) | 139 (1.030) | 106/492 | 0.4 | 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 | = 3186081 | NA (NA) | 149 (1.100) | 123/494 | 0.1 | 99.3% | coding (26/2466 nt) | Y75_RS15850 | fimbrial biogenesis outer membrane usher protein |
| ? | NC_007779 | 3512753 = | 1 (0.010) | coding (529/1026 nt) | cytR | DNA‑binding transcriptional regulator CytR | |||||
| * | ? | NC_007779 | = 3512759 | 8 (0.060) | 125 (0.930) | 102/494 | 0.6 | 94.0% | 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) | 151 (1.110) | 121/496 | 0.1 | 97.4% | intergenic (‑46/+30) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ |
| ? | NC_007779 | 3903274 = | 4 (0.030) | coding (37/825 nt) | Y75_RS19350 | protein bax | |||||
| * | ? | NC_007779 | 3746912 = | NA (NA) | 119 (0.880) | 101/494 | 0.6 | 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 | = 3748105 | NA (NA) | 121 (0.890) | 99/496 | 0.7 | 98.4% | intergenic (+146/+3) | Y75_RS18585/tnaB | IS5‑like element IS5 family transposase/low affinity tryptophan permease TnaB |
| ? | NC_007779 | 3982165 = | 2 (0.010) | intergenic (‑116/+683) | gadE/hdeD | acid resistance transcriptional activator GadE/acid‑resistance protein HdeD | |||||
| * | ? | NC_007779 | = 3903279 | 8 (0.060) | 128 (0.950) | 112/494 | 0.3 | 94.1% | 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) | 172 (1.280) | 124/492 | 0.1 | 98.3% | coding (748/783 nt) | Y75_RS19730 | hypothetical protein |
| ? | NC_007779 | = 4547133 | 3 (0.020) | coding (417/597 nt) | fimE | type 1 fimbria regulatory protein FimE | |||||
| * | ? | NC_007779 | = 3988378 | NA (NA) | 146 (1.080) | 114/494 | 0.3 | 99.3% | coding (747/783 nt) | Y75_RS19730 | hypothetical protein |
| ? | NC_007779 | 3989659 = | 1 (0.010) | intergenic (‑535/+94) | Y75_RS19730/arsC | hypothetical protein/glutaredoxin‑dependent arsenate reductase | |||||
| * | ? | NC_007779 | = 3988379 | NA (NA) | 120 (0.890) | 102/496 | 0.6 | 98.4% | coding (746/783 nt) | Y75_RS19730 | hypothetical protein |
| ? | NC_007779 | 4495464 = | 2 (0.010) | coding (356/999 nt) | idnR | DNA‑binding transcriptional regulator IdnR | |||||
| * | ? | NC_007779 | 4218985 = | 4 (0.030) | 111 (0.820) | 95/494 | 0.8 | 96.5% | 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 | 4 (0.030) | 173 (1.280) | 124/496 | 0.1 | 97.7% | 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) | 139 (1.030) | 117/496 | 0.2 | 97.2% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4495467 | 4 (0.030) | coding (353/999 nt) | idnR | DNA‑binding transcriptional regulator IdnR | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 92 (0.680) | 75/496 | 2.2 | 96.8% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4540919 | 3 (0.020) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 198 (1.460) | 122/496 | 0.1 | 98.0% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 4547128 = | 4 (0.030) | coding (412/597 nt) | fimE | type 1 fimbria regulatory protein FimE | |||||
| * | ? | NC_007779 | = 4311556 | NA (NA) | 140 (1.040) | 110/494 | 0.3 | 99.3% | intergenic (+145/+1) | Y75_RS21310/alsK | IS5‑like element IS5 family transposase/allose kinase |
| ? | NC_007779 | 4540915 = | 1 (0.010) | intergenic (+204/+379) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | 4547362 = | 71 (0.520) | 110 (0.840) | 97/478 | 0.6 | 62.3% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 65 (0.500) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 4547370 | 71 (0.520) | 89 (0.680) | 76/478 | 1.8 | 57.2% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 65 (0.500) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||