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 | 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 |
| MC JC | 1,301,041 | Δ1,336 bp | Y75_RS06530–Y75_RS06530 | Y75_RS06530, Y75_RS06530 | |
| RA | 1,372,264 | A→G | E112G (GAG→GGG) | Y75_RS06905 → | sugar phosphorylase |
| 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 |
| JC | 2,288,259 | (TTATCGCCT)2→3 | coding (550/1761 nt) | pbgA → | cardiolipin transport protein PbgA |
| 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 |
| RA | 3,531,979 | G→A | G92S (GGC→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 | |
| MC JC | 3,958,123 | Δ34 bp | coding (1156‑1189/1287 nt) | Y75_RS19595 → | C4‑dicarboxylate transporter DctC |
| RA | 4,136,677 | G→T | V191V (GTC→GTA) | frlD ← | fructoselysine 6‑kinase |
| RA | 4,221,755 | G→A | A353T (GCA→ACA) | aceA → | isocitrate lyase |
| 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 |
| JC | 4,547,860 | (TCCCTCAGTTCTACAGCGGCTCTG)1→2 | coding (66/549 nt) | fimA → | 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 | 1197828 | 1213107 | 15280 | 65 [62] | [64] 65 | [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] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 273179 = | NA (NA) | 131 (1.110) | 106/496 | 0.2 | 98.5% | intergenic (+2/+146) | Y75_RS01330/Y75_RS01335 | hypothetical protein/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 736805 = | 2 (0.020) | intergenic (+164/‑62) | Y75_RS03640/Y75_RS03645 | hypothetical protein/ISAs1 family transposase | |||||
| * | ? | NC_007779 | 273179 = | NA (NA) | 120 (1.020) | 100/496 | 0.3 | 99.2% | intergenic (+2/+146) | Y75_RS01330/Y75_RS01335 | hypothetical protein/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 991031 = | 1 (0.010) | intergenic (‑253/‑13) | pncB/pepN | nicotinate phosphoribosyltransferase/aminopeptidase N | |||||
| * | ? | NC_007779 | = 274373 | NA (NA) | 108 (0.920) | 94/496 | 0.5 | 97.3% | intergenic (‑32/‑176) | Y75_RS01335/mmuP | IS5‑like element IS5 family transposase/S‑methylmethionine permease |
| ? | NC_007779 | = 736808 | 3 (0.030) | intergenic (+167/‑59) | Y75_RS03640/Y75_RS03645 | hypothetical protein/ISAs1 family transposase | |||||
| * | ? | NC_007779 | = 274373 | NA (NA) | 121 (1.030) | 102/496 | 0.3 | 98.4% | intergenic (‑32/‑176) | Y75_RS01335/mmuP | IS5‑like element IS5 family transposase/S‑methylmethionine permease |
| ? | NC_007779 | = 991034 | 2 (0.020) | intergenic (‑256/‑10) | pncB/pepN | nicotinate phosphoribosyltransferase/aminopeptidase N | |||||
| * | ? | NC_007779 | 380484 = | NA (NA) | 128 (1.090) | 112/496 | 0.1 | 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) | 99 (0.850) | 89/492 | 0.6 | 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 | = 1398952 | NA (NA) | 116 (0.990) | 101/496 | 0.3 | 100% | intergenic (+146/‑127) | Y75_RS07025/Y75_RS07030 | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NC_007779 | = 1908959 | 0 (0.000) | coding (191/210 nt) | cspE | transcription antiterminator/RNA stability regulator CspE | |||||
| * | ? | NC_007779 | 1429311 = | 129 (1.100) | 117 (1.010) | 105/490 | 0.2 | 64.7% | pseudogene (209/216 nt) | Y75_RS07225 | Ail/Lom family outer membrane beta‑barrel protein |
| ? | NC_007779 | = 3361428 | 0 (0.000) | coding (398/765 nt) | Y75_RS16705 | DUF1120 domain‑containing protein | |||||
| * | ? | NC_007779 | = 1430508 | 93 (0.790) | 111 (0.940) | 99/496 | 0.3 | 70.0% | intergenic (‑68/‑2) | Y75_RS07230/Y75_RS07235 | IS5‑like element ISKpn26 family transposase/Ail/Lom family outer membrane beta‑barrel protein |
| ? | NC_007779 | 3361427 = | 2 (0.020) | coding (397/765 nt) | Y75_RS16705 | DUF1120 domain‑containing protein | |||||
| * | ? | NC_007779 | 1908956 = | 2 (0.020) | 124 (1.050) | 105/496 | 0.2 | 98.4% | coding (194/210 nt) | cspE | transcription antiterminator/RNA stability regulator CspE |
| ? | NC_007779 | 2176983 = | NA (NA) | intergenic (‑3/‑32) | gatA/Y75_RS10980 | PTS galactitol transporter subunit IIA/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 3186081 | NA (NA) | 130 (1.110) | 107/494 | 0.2 | 99.2% | 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 | 2 (0.020) | 119 (1.020) | 102/494 | 0.2 | 98.4% | 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) | 146 (1.240) | 126/496 | 0.0 | 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 | 3746912 = | NA (NA) | 179 (1.530) | 111/494 | 0.1 | 99.5% | intergenic (‑4/‑31) | Y75_RS18580/Y75_RS18585 | tryptophan permease/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 3840031 = | 1 (0.010) | coding (582/699 nt) | rfaY | lipopolysaccharide core heptose(II) kinase RfaY | |||||
| * | ? | NC_007779 | = 3748105 | NA (NA) | 127 (1.080) | 108/496 | 0.2 | 99.2% | intergenic (+146/+3) | Y75_RS18585/tnaB | IS5‑like element IS5 family transposase/low affinity tryptophan permease TnaB |
| ? | NC_007779 | = 3840035 | 1 (0.010) | coding (586/699 nt) | rfaY | lipopolysaccharide core heptose(II) kinase RfaY | |||||
| * | ? | NC_007779 | = 3903279 | 6 (0.050) | 124 (1.060) | 99/494 | 0.3 | 95.4% | 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 | 3909304 = | 1 (0.010) | 167 (1.420) | 128/496 | 0.0 | 99.4% | intergenic (‑20/‑346) | Y75_RS19370/xylA | D‑xylose ABC transporter substrate‑binding protein/xylose isomerase |
| ? | NC_007779 | = 3988379 | NA (NA) | coding (746/783 nt) | Y75_RS19730 | hypothetical protein | |||||
| * | ? | NC_007779 | = 3909307 | 3 (0.030) | 145 (1.230) | 117/496 | 0.1 | 98.0% | intergenic (‑23/‑343) | Y75_RS19370/xylA | D‑xylose ABC transporter substrate‑binding protein/xylose isomerase |
| ? | NC_007779 | 3987185 = | NA (NA) | pseudogene (3/379 nt) | Y75_RS19720 | hypothetical protein | |||||
| * | ? | NC_007779 | 3987185 = | NA (NA) | 108 (0.920) | 103/496 | 0.2 | 95.6% | pseudogene (3/379 nt) | Y75_RS19720 | hypothetical protein |
| ? | NC_007779 | = 4544238 | 5 (0.040) | intergenic (‑57/‑1399) | nanC/fimB | N‑acetylneuraminic acid outer membrane channel NanC/type 1 fimbria regulatory protein FimB | |||||
| * | ? | NC_007779 | = 3988379 | NA (NA) | 142 (1.210) | 122/496 | 0.0 | 97.9% | coding (746/783 nt) | Y75_RS19730 | hypothetical protein |
| ? | NC_007779 | 4544235 = | 3 (0.030) | intergenic (‑54/‑1402) | nanC/fimB | N‑acetylneuraminic acid outer membrane channel NanC/type 1 fimbria regulatory protein FimB | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 74 (0.630) | 66/496 | 2.1 | 93.7% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4540919 | 5 (0.040) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 119 (1.010) | 103/496 | 0.2 | 99.2% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 4546841 = | 1 (0.010) | coding (125/597 nt) | fimE | type 1 fimbria regulatory protein FimE | |||||
| * | ? | NC_007779 | = 4311556 | NA (NA) | 126 (1.080) | 108/494 | 0.1 | 97.7% | intergenic (+145/+1) | Y75_RS21310/alsK | IS5‑like element IS5 family transposase/allose kinase |
| ? | NC_007779 | 4540915 = | 3 (0.030) | intergenic (+204/+379) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | = 4311557 | NA (NA) | 148 (1.260) | 114/496 | 0.1 | 98.7% | pseudogene (921/921 nt) | alsK | allose kinase |
| ? | NC_007779 | = 4546844 | 2 (0.020) | coding (128/597 nt) | fimE | type 1 fimbria regulatory protein FimE | |||||
| * | ? | NC_007779 | 4547362 = | 37 (0.310) | 85 (0.750) | 75/478 | 1.2 | 71.5% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 32 (0.280) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 4547370 | 37 (0.310) | 84 (0.740) | 73/478 | 1.3 | 71.3% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 32 (0.280) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||