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 | 575,023 | C→T | 22.4% | G10G (GGG→GGA) | EK12AG100_RS02845 ← | IS5‑like element IS5 family transposase |
| RA | 576,212 | A→G | 49.5% | H108H (CAT→CAC) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,226 | C→T | 50.5% | V104I (GTT→ATT) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,326 | G→A | 48.4% | N70N (AAC→AAT) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,398 | G→A | 46.9% | I46I (ATC→ATT) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,443 | G→A | 47.8% | N31N (AAC→AAT) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,481 | C→T | 46.8% | D19N (GAC→AAC) | EK12AG100_RS02865 ← | DUF1398 domain‑containing protein |
| RA | 576,592 | T→C | 49.7% | intergenic (‑57/‑229) | EK12AG100_RS02865 ← / → EK12AG100_RS02870 | DUF1398 domain‑containing protein/hypothetical protein |
| RA | 576,612 | T→C | 50.7% | intergenic (‑77/‑209) | EK12AG100_RS02865 ← / → EK12AG100_RS02870 | DUF1398 domain‑containing protein/hypothetical protein |
| RA | 576,658 | C→A | 48.1% | intergenic (‑123/‑163) | EK12AG100_RS02865 ← / → EK12AG100_RS02870 | DUF1398 domain‑containing protein/hypothetical protein |
| RA | 576,752 | T→C | 48.0% | intergenic (‑217/‑69) | EK12AG100_RS02865 ← / → EK12AG100_RS02870 | DUF1398 domain‑containing protein/hypothetical protein |
| RA | 576,961 | A→G | 44.4% | R47R (AGA→AGG) | EK12AG100_RS02870 → | hypothetical protein |
| RA | 577,056 | T→C | 48.7% | intergenic (+29/+136) | EK12AG100_RS02870 → / ← EK12AG100_RS02875 | hypothetical protein/YlcI/YnfO family protein |
| RA | 577,060 | A→G | 51.5% | intergenic (+33/+132) | EK12AG100_RS02870 → / ← EK12AG100_RS02875 | hypothetical protein/YlcI/YnfO family protein |
| RA | 577,061 | C→T | 51.3% | intergenic (+34/+131) | EK12AG100_RS02870 → / ← EK12AG100_RS02875 | hypothetical protein/YlcI/YnfO family protein |
| RA | 577,243 | T→C | 54.3% | R48R (AGA→AGG) | EK12AG100_RS02875 ← | YlcI/YnfO family protein |
| RA | 577,378 | A→C | 31.3% | 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 | 12.4% | intergenic (‑301/‑88) | EK12AG100_RS02875 ← / → EK12AG100_RS02885 | YlcI/YnfO family protein/DNA‑packaging protein |
| RA | 577,771 | T→A | 31.4% | intergenic (‑385/‑4) | EK12AG100_RS02875 ← / → EK12AG100_RS02885 | YlcI/YnfO family protein/DNA‑packaging protein |
| RA | 577,772 | G→A | 31.3% | intergenic (‑386/‑3) | EK12AG100_RS02875 ← / → EK12AG100_RS02885 | YlcI/YnfO family protein/DNA‑packaging protein |
| RA | 577,983 | G→T | 42.8% | R70L (CGG→CTG) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 577,997 | G→A | 40.3% | A75T (GCA→ACA) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,014 | G→A | 61.2% | G80G (GGG→GGA) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,059 | C→T | 39.8% | D95D (GAC→GAT) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,068 | A→G | 38.4% | E98E (GAA→GAG) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,074 | A→G | 61.8% | K100K (AAA→AAG) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,126 | T→C | 42.1% | L118L (TTG→CTG) | EK12AG100_RS02885 → | DNA‑packaging protein |
| RA | 578,168 | C→A | 42.1% | L132I (CTC→ATC) | EK12AG100_RS02885 → | DNA‑packaging protein |
| 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 |
| MC JC | 1,438,121 | Δ493 bp | 100% | [ttcA] | [ttcA] | |
| RA | 1,619,412 | C→A | 7.3% | 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 | 33.2% | 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 | 25.0% | R70L (CGG→CTG) | EK12AG100_RS08170 ← | DNA‑packaging protein |
| RA | 1,639,827 | T→C | 23.0% | E65E (GAA→GAG) | EK12AG100_RS08170 ← | DNA‑packaging protein |
| RA | 1,640,036 | A→C | 61.6% | intergenic (‑15/‑374) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,640,067 | C→A | 40.5% | intergenic (‑46/‑343) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,640,077 | T→C | 42.3% | intergenic (‑56/‑333) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,640,109 | G→A | 46.2% | intergenic (‑88/‑301) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,640,138 | T→C | 52.8% | intergenic (‑117/‑272) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,640,157 | C→T | 52.3% | intergenic (‑136/‑253) | EK12AG100_RS08170 ← / → EK12AG100_RS08175 | DNA‑packaging protein/YlcI/YnfO family protein |
| RA | 1,791,936 | A→T | 5.2% | intergenic (+4/‑153) | ppsR → / → aroH | posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR/3‑deoxy‑7‑phosphoheptulonate synthase AroH |
| MC JC | 2,561,554 | Δ90 bp | 100% | [EK12AG100_RS12790]–EK12AG100_RS25715 | [EK12AG100_RS12790], EK12AG100_RS25715 | |
| RA | 3,067,161 | T→G | 100% | K129N (AAA→AAC) | fbaA ← | class II fructose‑bisphosphate aldolase |
| RA | 3,940,810 | C→T | 100% | noncoding (604/2886 nt) | EK12AG100_RS19545 → | 23S ribosomal RNA |
| RA | 4,022,771 | T→G | 41.3% | Y437* (TAT→TAG) | ubiD → | 4‑hydroxy‑3‑polyprenylbenzoate decarboxylase |
| RA | 4,023,909 | T→G | 67.5% | intergenic (+208/+173) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,921 | G→A | 59.9% | intergenic (+220/+161) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,922 | T→G | 59.9% | intergenic (+221/+160) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,931 | A→T | 43.7% | intergenic (+230/+151) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,933 | A→G | 43.8% | intergenic (+232/+149) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,935:1 | +G | 43.8% | intergenic (+234/+147) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,937:1 | +G | 37.5% | intergenic (+236/+145) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,940 | A→T | 37.3% | intergenic (+239/+142) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,942 | C→G | 37.5% | intergenic (+241/+140) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,947 | G→A | 33.2% | intergenic (+246/+135) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| RA | 4,023,962 | T→C | 23.5% | intergenic (+261/+120) | EK12AG100_RS19960 → / ← fadA | NAD(P)H‑flavin reductase/acetyl‑CoA C‑acyltransferase FadA |
| 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 | 100% | intergenic (+474/+168) | 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 | 4,539,461 | Δ1 bp | 9.1% | intergenic (+354/‑128) | 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 | |||
| * | * | ÷ | NZ_LN832404 | 575054 | 575300–575153 | 100–247 | 183 [1] | [59] 61 | [rzoD] | [rzoD] |
| * | * | ÷ | NZ_LN832404 | 822804–822904 | 822992 | 89–189 | 61 [59] | [0] 124 | [rzoD]–[EK12AG100_RS04195] | [rzoD],[EK12AG100_RS04195] |
| * | * | ÷ | NZ_LN832404 | 1982224 | 1982362 | 139 | 60 [59] | [0] 179 | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
| * | * | ÷ | NZ_LN832404 | 3127805 | 3127964 | 160 | 60 [59] | [2] 177 | EK12AG100_RS15510/EK12AG100_RS15515 | IS5‑like element IS5 family transposase/lipopolysaccharide biosynthesis protein |
| * | * | ÷ | NZ_LN832404 | 3420277–3420746 | 3421059–3420750 | 5–783 | 60 [59] | [59] 61 | [rrf]–[EK12AG100_RS17000] | [rrf],[EK12AG100_RS17000] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_LN832404 | = 61489 | 0 (0.000) | 78 (0.940) | 70/416 | 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) | 96 (1.200) | 83/400 | 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) | 138 (1.210) | 116/572 | NT | 47.3% | intergenic (‑32/‑176) | EK12AG100_RS01335/mmuP | IS5‑like element IS5 family transposase/S‑methylmethionine permease |
| ? | NZ_LN832404 | 576125 = | 154 (1.350) | coding (411/411 nt) | EK12AG100_RS02865 | DUF1398 domain‑containing protein | |||||
| * | ? | NZ_LN832404 | = 381810 | NA (NA) | 89 (1.080) | 78/414 | 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 | = 575053 | 0 (0.000) | 153 (1.460) | 25/526 | NT | 100% | intergenic (‑1/‑216) | EK12AG100_RS02845/rzoD | IS5‑like element IS5 family transposase/prophage lysis lipoprotein RzoD |
| ? | NZ_LN832404 | 1982363 = | 0 (0.000) | intergenic (‑330/‑326) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
| * | ? | NZ_LN832404 | = 578602 | 133 (1.170) | 79 (1.010) | 71/394 | NT | 63.3% | 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) | 89 (1.110) | 82/404 | 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) | 123 (1.190) +27 bp |
111/518 | 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) | 71 (0.890) | 66/400 | 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) | 103 (1.040) | 93/496 | 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) | 80 (1.030) | 72/390 | 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 | 2069112 = | 144 (1.260) | 143 (1.620) | 86/444 | NT | 71.9% | 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) | 95 (0.940) +32 bp |
84/508 | 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) | 82 (1.050) | 74/392 | 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 | 3423324 = | 0 (0.000) | 106 (1.320) | 85/402 | NT | 70.0% | intergenic (‑20/+146) | EK12AG100_RS17000/EK12AG100_RS17005 | 23S ribosomal RNA/tRNA‑Ala |
| ? | NZ_LN832404 | 4206479 = | 91 (1.140) | intergenic (+157/‑28) | EK12AG100_RS20830/EK12AG100_RS20835 | tRNA‑Glu/23S ribosomal RNA | |||||