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 | freq | annotation | gene | description |
| RA | 15,571 | T→C | 100% | L43L (TTG→CTG) | EK12AG100_RS00080 → | IS4‑like element IS421 family transposase |
| RA | 384,896 | A→C | 100% | G122G (GGA→GGC) | tauA → | taurine ABC transporter substrate‑binding protein |
| RA | 472,148 | A→G | 100% | G84G (GGA→GGG) | glnK → | P‑II family nitrogen regulator |
| RA | 576,212 | A→G | 47.7% | H108H (CAT→CAC) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,226 | C→T | 48.5% | V104I (GTT→ATT) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,326 | G→A | 45.5% | N70N (AAC→AAT) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,398 | G→A | 48.3% | I46I (ATC→ATT) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,443 | G→A | 47.5% | N31N (AAC→AAT) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,481 | C→T | 47.3% | D19N (GAC→AAC) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,592 | T→C | 52.0% | intergenic (‑57/‑229) | EK12AG100_RS02865 ← / → EK12AG100_RS02870 | DUF1398 domain‑containing protein/hypothetical protein |
| RA | 576,612 | T→C | 48.1% | intergenic (‑77/‑209) | EK12AG100_RS02865 ← / → EK12AG100_RS02870 | DUF1398 domain‑containing protein/hypothetical protein |
| RA | 576,658 | C→A | 51.9% | intergenic (‑123/‑163) | EK12AG100_RS02865 ← / → EK12AG100_RS02870 | DUF1398 domain‑containing protein/hypothetical protein |
| RA | 576,752 | T→C | 50.8% | intergenic (‑217/‑69) | EK12AG100_RS02865 ← / → EK12AG100_RS02870 | DUF1398 domain‑containing protein/hypothetical protein |
| RA | 576,961 | A→G | 52.6% | R47R (AGA→AGG) | EK12AG100_RS02870 → | hypothetical protein |
| RA | 577,056 | T→C | 49.4% | intergenic (+29/+136) | EK12AG100_RS02870 → / ← EK12AG100_RS02875 | hypothetical protein/YlcI/YnfO family protein |
| RA | 577,060 | A→G | 49.7% | intergenic (+33/+132) | EK12AG100_RS02870 → / ← EK12AG100_RS02875 | hypothetical protein/YlcI/YnfO family protein |
| RA | 577,061 | C→T | 49.7% | intergenic (+34/+131) | EK12AG100_RS02870 → / ← EK12AG100_RS02875 | hypothetical protein/YlcI/YnfO family protein |
| RA | 577,243 | T→C | 54.5% | R48R (AGA→AGG) | EK12AG100_RS02875 ← | YlcI/YnfO family protein |
| RA | 577,378 | A→C | 29.4% | T3T (ACT→ACG) | EK12AG100_RS02875 ← | YlcI/YnfO family protein |
| RA | 577,658 | A→G | 100% | intergenic (‑272/‑117) | EK12AG100_RS02875 ← / → EK12AG100_RS02885 | YlcI/YnfO family protein/DNA‑packaging protein |
| RA | 577,687 | C→T | 8.1% | intergenic (‑301/‑88) | EK12AG100_RS02875 ← / → EK12AG100_RS02885 | YlcI/YnfO family protein/DNA‑packaging protein |
| RA | 577,771 | T→A | 23.8% | intergenic (‑385/‑4) | EK12AG100_RS02875 ← / → EK12AG100_RS02885 | YlcI/YnfO family protein/DNA‑packaging protein |
| RA | 577,772 | G→A | 23.6% | intergenic (‑386/‑3) | EK12AG100_RS02875 ← / → EK12AG100_RS02885 | YlcI/YnfO family protein/DNA‑packaging protein |
| RA | 577,983 | G→T | 39.4% | R70L (CGG→CTG) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 577,997 | G→A | 37.4% | A75T (GCA→ACA) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,014 | G→A | 64.0% | G80G (GGG→GGA) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,059 | C→T | 27.7% | D95D (GAC→GAT) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,068 | A→G | 25.5% | E98E (GAA→GAG) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,074 | A→G | 72.3% | K100K (AAA→AAG) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,126 | T→C | 24.2% | L118L (TTG→CTG) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,168 | C→A | 26.5% | L132I (CTC→ATC) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 722,802 | C→A | 5.4% | M392I (ATG→ATT) | kdpB ← | potassium‑transporting ATPase subunit KdpB |
| RA | 1,015,338 | A→C | 100% | L202V (TTA→GTA) | elyC ← | envelope biogenesis factor ElyC |
| RA | 1,123,847 | G→A | 100% | intergenic (+494/‑49) | putP → / → EK12AG100_RS05615 | sodium/proline symporter PutP/FTR1 family protein |
| MC JC | 1,238,818 | Δ84 bp | 100% | coding (1156‑1239/1335 nt) | EK12AG100_RS06230 → | NADP‑dependent isocitrate dehydrogenase |
| RA | 1,363,615 | A→G | 100% | S522G (AGC→GGC) | acnA → | aconitate hydratase AcnA |
| RA | 1,364,782 | G→A | 5.3% | intergenic (+55/+9) | acnA → / ← ribA | aconitate hydratase AcnA/GTP cyclohydrolase II |
| RA | 1,505,339 | Δ1 bp | 6.1% | coding (124/594 nt) | tehB → | tellurite resistance methyltransferase TehB |
| RA | 1,619,412 | C→A | 7.1% | intergenic (+73/‑5) | EK12AG100_RS08055 → / → yneK | LysR family transcriptional regulator/putative protein YneK |
| RA | 1,639,728 | T→C | 100% | E98E (GAA→GAG) | EK12AG100_RS08170 ← | DNA‑packaging protein |
| RA | 1,639,737 | G→A | 20.5% | D95D (GAC→GAT) | EK12AG100_RS08170 ← | DNA‑packaging protein |
| RA | 1,639,799 | C→T | 100% | A75T (GCA→ACA) | EK12AG100_RS08170 ← | DNA‑packaging protein |
| RA | 1,639,813 | C→A | 9.0% | R70L (CGG→CTG) | EK12AG100_RS08170 ← | DNA‑packaging protein |
| RA | 1,640,036 | A→C | 57.3% | intergenic (‑15/‑374) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,640,067 | C→A | 50.1% | intergenic (‑46/‑343) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,640,077 | T→C | 49.1% | intergenic (‑56/‑333) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,640,109 | G→A | 53.4% | intergenic (‑88/‑301) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,640,138 | T→C | 43.0% | intergenic (‑117/‑272) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,640,157 | C→T | 42.2% | intergenic (‑136/‑253) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 2,115,974 | G→A | 5.0% | G8G (GGC→GGT) | rfbB ← | dTDP‑glucose 4,6‑dehydratase |
| MC JC | 2,561,554 | Δ90 bp | 100% | [EK12AG100_RS12790]–EK12AG100_RS25715 | [EK12AG100_RS12790], EK12AG100_RS25715 | |
| RA | 2,563,059 | A→G | 5.6% | M1A (GTG→GCG) † *409R (TGA→CGA) |
eutA ← eutH ← |
ethanolamine ammonia‑lyase reactivating factor EutA ethanolamine utilization protein EutH |
| RA | 2,574,065 | C→T | 6.2% | Q163Q (CAG→CAA) | EK12AG100_RS12855 ← | NADP‑dependent oxaloacetate‑decarboxylating malate dehydrogenase |
| RA | 2,756,267 | A→G | 5.2% | M327V (ATG→GTG) | EK12AG100_RS13710 → | DUF3987 domain‑containing protein |
| RA | 3,067,161 | T→G | 100% | K129N (AAA→AAC) | fbaA ← | class II fructose‑bisphosphate aldolase |
| RA | 3,118,183 | G→A | 5.3% | I642I (ATC→ATT) | glcB ← | malate synthase G |
| RA | 4,022,771 | T→G | 57.7% | Y437* (TAT→TAG) | ubiD → | 4‑hydroxy‑3‑polyprenylbenzoate decarboxylase |
| RA | 4,023,909 | T→G | 100% | intergenic (+208/+173) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,962 | T→C | 39.1% | intergenic (+261/+120) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,033,969 | A→T | 41.5% | intergenic (+161/‑14) | EK12AG100_RS20005 → / → EK12AG100_RS20010 | tRNA‑Ala/23S ribosomal RNA |
| RA | 4,061,440 | A→G | 6.1% | L267P (CTG→CCG) | EK12AG100_RS20130 ← | MFS transporter |
| RA | 4,220,111 | T→C | 100% | intergenic (‑10/‑190) | iclR ← / → metH | glyoxylate bypass operon transcriptional repressor IclR/methionine synthase |
| RA | 4,264,972 | T→A | 100% | intergenic (+192/+310) | EK12AG100_RS21080 → / ← EK12AG100_RS25365 | aromatic amino acid transaminase/hypothetical protein |
| RA | 4,292,533 | T→C | 100% | intergenic (+266/+376) | gltP → / ← EK12AG100_RS21205 | glutamate/aspartate:proton symporter GltP/sel1 repeat family protein |
| RA | 4,292,741 | C→T | 65.8% | intergenic (+474/+168) | gltP → / ← EK12AG100_RS21205 | glutamate/aspartate:proton symporter GltP/sel1 repeat family protein |
| RA | 4,292,759 | C→T | 11.7% | intergenic (+492/+150) | gltP → / ← EK12AG100_RS21205 | glutamate/aspartate:proton symporter GltP/sel1 repeat family protein |
| RA | 4,292,853:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← EK12AG100_RS21205 | glutamate/aspartate:proton symporter GltP/sel1 repeat family protein |
| RA | 4,457,594 | C→A | 5.9% | R514L (CGC→CTC) | nrdD ← | anaerobic ribonucleoside‑triphosphate reductase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_LN832404 | 574087–575030 | 575321 | 292–1235 | 38 [34] | [35] 36 | [EK12AG100_RS02845]–[rzoD] | [EK12AG100_RS02845],[rzoD] |
| * | * | ÷ | NZ_LN832404 | 822785 | 822992 | 208 | 36 [34] | [0] 89 | [rzoD]–[EK12AG100_RS04195] | [rzoD],[EK12AG100_RS04195] |
| * | * | ÷ | NZ_LN832404 | 1438475 | 1438697 | 223 | 38 [35] | [35] 38 | ttcA/uspF | tRNA 2‑thiocytidine(32) synthetase TtcA/universal stress protein UspF |
| * | * | ÷ | NZ_LN832404 | 1982242 | 1982339 | 98 | 36 [34] | [0] 208 | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
| * | * | ÷ | NZ_LN832404 | 3420298–3420745 | 3421004–3420750 | 6–707 | 37 [33] | [34] 36 | [EK12AG100_RS17000] | [EK12AG100_RS17000] |
| * | * | ÷ | NZ_LN832404 | 3940783–3942180 | 3942180 | 1–1398 | 36 [35] | [35] 36 | EK12AG100_RS19545 | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_LN832404 | = 61489 | 0 (0.000) | 71 (1.270) | 63/370 | NT | 100% | intergenic (‑76/+87) | EK12AG100_RS23030/rapA | RNA polymerase‑associated protein RapA/RNA polymerase‑associated protein RapA |
| ? | NZ_LN832404 | = 381811 | NA (NA) | coding (847/914 nt) | EK12AG100_RS01865 | IS3‑like element IS2 family transposase | |||||
| * | ? | NZ_LN832404 | 61489 = | 0 (0.000) | 40 (0.750) | 34/354 | NT | 100% | intergenic (‑76/+87) | EK12AG100_RS23030/rapA | RNA polymerase‑associated protein RapA/RNA polymerase‑associated protein RapA |
| ? | NZ_LN832404 | 380645 = | NA (NA) | coding (41/361 nt) | EK12AG100_RS01865 | IS3‑like element IS2 family transposase | |||||
| * | ? | NZ_LN832404 | = 274541 | NA (NA) | 104 (1.310) | 90/526 | NT | 47.1% | intergenic (‑32/‑176) | EK12AG100_RS01335/mmuP | IS5‑like element IS5 family transposase/S‑methylmethionine permease |
| ? | NZ_LN832404 | 576125 = | 117 (1.470) | coding (411/411 nt) | EK12AG100_RS02865 | DUF1398 domain‑containing protein | |||||
| * | ? | NZ_LN832404 | = 381810 | NA (NA) | 41 (0.740) | 39/368 | NT | 100% | coding (846/914 nt) | EK12AG100_RS01865 | IS3‑like element IS2 family transposase |
| ? | NZ_LN832404 | = 932184 | 0 (0.000) | intergenic (‑74/‑445) | EK12AG100_RS04715/EK12AG100_RS04720 | aspartate:alanine antiporter/hypothetical protein | |||||
| * | ? | NZ_LN832404 | = 578602 | 81 (1.020) | 55 (1.050) | 52/348 | NT | 67.3% | coding (308/744 nt) | EK12AG100_RS02890 | phage terminase large subunit family protein |
| ? | NZ_LN832404 | 822993 = | 0 (0.000) | coding (129/1746 nt) | EK12AG100_RS04195 | phage terminase large subunit family protein | |||||
| * | ? | NZ_LN832404 | 932185 = | 0 (0.000) | 54 (1.000) | 51/358 | NT | 100% | intergenic (‑75/‑444) | EK12AG100_RS04715/EK12AG100_RS04720 | aspartate:alanine antiporter/hypothetical protein |
| ? | NZ_LN832404 | = 1472810 | NA (NA) | coding (39/361 nt) | EK12AG100_RS07405 | IS3‑like element IS2 family transposase | |||||
| * | ? | NZ_LN832404 | = 1423461 | NA (NA) | 89 (1.250) +27 bp |
77/472 | NT | 100% | intergenic (+148/‑125) | EK12AG100_RS07185/EK12AG100_RS07190 | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NZ_LN832404 | = 2242224 | 0 (0.000) | intergenic (‑1/+2) | mglA/mglB | galactose/methyl galactoside ABC transporter ATP‑binding protein MglA/galactose/glucose ABC transporter substrate‑binding protein MglB | |||||
| * | ? | NZ_LN832404 | = 1472808 | NA (NA) | 70 (1.310) | 62/354 | NT | 100% | coding (41/361 nt) | EK12AG100_RS07405 | IS3‑like element IS2 family transposase |
| ? | NZ_LN832404 | = 1870685 | 0 (0.000) | intergenic (‑559/‑65) | EK12AG100_RS09380/EK12AG100_RS09385 | scaffolding protein MipA/protein kinase YeaG | |||||
| * | ? | NZ_LN832404 | = 1474132 | NA (NA) | 69 (1.020) | 65/450 | NT | 100% | coding (1121/1152 nt) | EK12AG100_RS07415 | IS30‑like element IS30 family transposase |
| ? | NZ_LN832404 | 2694668 = | 0 (0.000) | intergenic (‑89/+37) | yfhb/EK12AG100_RS25720 | phosphatidylglycerophosphatase C/phosphatidylglycerophosphatase C | |||||
| * | ? | NZ_LN832404 | = 1655111 | NA (NA) | 38 (0.730) | 38/344 | NT | 100% | pseudogene (616/696 nt) | EK12AG100_RS08315 | IS3‑like element IS2 family transposase |
| ? | NZ_LN832404 | 1870686 = | 0 (0.000) | intergenic (‑560/‑64) | EK12AG100_RS09380/EK12AG100_RS09385 | scaffolding protein MipA/protein kinase YeaG | |||||
| * | ? | NZ_LN832404 | 1982340 = | 0 (0.000) | 190 (2.390) | 17/526 | NT | 100% | intergenic (‑307/‑349) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
| ? | NZ_LN832404 | = 2070235 | NA (NA) | coding (23/1017 nt) | EK12AG100_RS10470 | IS5‑like element IS5 family transposase | |||||
| * | ? | NZ_LN832404 | 2069112 = | 119 (1.500) | 198 (3.300) | 95/398 | NT | 81.5% | intergenic (‑117/+129) | EK12AG100_RS23990/EK12AG100_RS10470 | cobalamin biosynthesis protein/IS5‑like element IS5 family transposase |
| ? | NZ_LN832404 | 3127965 = | 0 (0.000) | intergenic (+468/+15) | EK12AG100_RS15510/EK12AG100_RS15515 | IS5‑like element IS5 family transposase/lipopolysaccharide biosynthesis protein | |||||
| * | ? | NZ_LN832404 | = 2105880 | NA (NA) | 84 (1.200) +32 bp |
77/462 | NT | 100% | intergenic (‑33/+2) | EK12AG100_RS10660/EK12AG100_RS10665 | IS5‑like element IS5 family transposase/glycosyltransferase |
| ? | NZ_LN832404 | 2242225 = | 0 (0.000) | intergenic (‑2/+1) | mglA/mglB | galactose/methyl galactoside ABC transporter ATP‑binding protein MglA/galactose/glucose ABC transporter substrate‑binding protein MglB | |||||
| * | ? | NZ_LN832404 | = 2694669 | 0 (0.000) | 37 (0.710) | 34/346 | NT | 100% | intergenic (‑90/+36) | yfhb/EK12AG100_RS25720 | phosphatidylglycerophosphatase C/phosphatidylglycerophosphatase C |
| ? | NZ_LN832404 | = 4505063 | NA (NA) | coding (29/1152 nt) | EK12AG100_RS22270 | IS30‑like element IS30 family transposase | |||||
| * | ? | NZ_LN832404 | 3927683 = | 73 (0.920) | 4 (0.050) | 4/526 | NT | 5.0% | intergenic (‑78/‑145) | ravA/EK12AG100_RS19490 | ATPase RavA/low affinity potassium transporter Kup |
| ? | NZ_LN832404 | = 4499989 | 78 (0.980) | intergenic (‑84/‑543) | EK12AG100_RS22240/EK12AG100_RS22245 | IS4‑like element IS4 family transposase/MFS transporter | |||||