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breseq version 0.24rc1 revision 83e50355436e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Marginal read alignment evidence... | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | position | change | freq | score | reads | annotation | genes | product | ||
* | REL606 | 3,351,171 | 0 | T→G | 100.0% | 4.9 | 6 | intergenic (+85/+144) | yhdZ/rrfF | predicted amino‑acid transporter subunit/5S ribosomal RNA |
* | REL606 | 1,602,101 | 0 | C→T | 100.0% | 2.1 | 3 | intergenic (+124/+104) | pinQ/ECB_01505 | predicted site‑specific recombinase/conserved hypothetical protein |
* | REL606 | 2,650,833 | 0 | T→C | 100.0% | 2.0 | 2 | intergenic (‑156/+29) | rrlG/gltW | 23S ribosomal RNA/tRNA‑Glu |
* | REL606 | 2,650,834 | 0 | C→A | 100.0% | 2.0 | 2 | intergenic (‑157/+28) | rrlG/gltW | 23S ribosomal RNA/tRNA‑Glu |
* | REL606 | 569,034 | 0 | G→A | 100.0% | 1.9 | 2 | 903 | yhhI | predicted transposase |
* | REL606 | 569,036 | 0 | T→A | 100.0% | 1.9 | 2 | 901 | yhhI | predicted transposase |
* | REL606 | 2,650,837 | 0 | C→T | 100.0% | 1.9 | 2 | intergenic (‑160/+25) | rrlG/gltW | 23S ribosomal RNA/tRNA‑Glu |
* | REL606 | 1,605,859 | 0 | A→C | 100.0% | 1.8 | 4 | 24 | stfR | predicted tail fiber protein |
* | REL606 | 1,110,599 | 0 | G→A | 100.0% | 1.7 | 2 | 777 | insF‑1 | putative transposase for IS3 |
* | REL606 | 2,650,849 | 0 | A→T | 100.0% | 1.7 | 2 | intergenic (‑172/+13) | rrlG/gltW | 23S ribosomal RNA/tRNA‑Glu |
* | REL606 | 2,650,839 | 0 | A→G | 100.0% | 1.5 | 2 | intergenic (‑162/+23) | rrlG/gltW | 23S ribosomal RNA/tRNA‑Glu |
* | REL606 | 569,294 | 0 | A→T | 100.0% | 1.4 | 2 | 643 | yhhI | predicted transposase |
* | REL606 | 2,842,128 | 0 | C→G | 100.0% | 1.4 | 3 | noncoding (13/77 nt) | metW | tRNA‑Met |
* | REL606 | 3,354,702 | 0 | G→T | 100.0% | 1.4 | 2 | intergenic (‑23/+161) | rrlD/alaU | 23S ribosomal RNA/tRNA‑Ala |
* | REL606 | 1,110,603 | 0 | C→T | 100.0% | 1.1 | 2 | 773 | insF‑1 | putative transposase for IS3 |
* | REL606 | 1,607,946 | 0 | G→T | 100.0% | 1.1 | 1 | intergenic (‑14/‑27) | ECB_01510/insE‑3 | putative tail component of prophage/putative transposase‑related protein |
* | REL606 | 1,545,116 | 0 | G→T | 100.0% | 1.0 | 2 | 881 | gadB | glutamate decarboxylase B, PLP‑dependent |
* | REL606 | 573,202 | 0 | T→G | 100.0% | 0.9 | 8 | 287 | ECB_00530 | conserved hypothetical protein |
* | REL606 | 2,453,978 | 0 | G→C | 100.0% | 0.7 | 2 | noncoding (52/76 nt) | valX | tRNA‑Val |
* | REL606 | 3,555,688 | 0 | A→G | 100.0% | 0.4 | 1 | 623 | yhhI | predicted transposase |
* | REL606 | 569,916 | 0 | C→A | 100.0% | 0.3 | 1 | 21 | yhhI | predicted transposase |
Marginal mixed read alignment evidence... | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | position | change | freq | score | reads | annotation | genes | product | ||
* | REL606 | 33,801 | 0 | T→G | 29.4% | 11.6 | 34 | 80 | carA | carbamoyl‑phosphate synthase small subunit |
* | REL606 | 87,812 | 0 | T→G | 38.5% | 21.7 | 52 | 641 | leuO | leucine transcriptional activator |
* | REL606 | 92,359 | 0 | G→T | 25.0% | 14.0 | 40 | intergenic (+523/‑79) | fruR/yabB | DNA‑binding transcriptional dual regulator/hypothetical protein |
* | REL606 | 93,946 | 0 | G→C | 36.7% | 19.0 | 50 | 111 | ftsL | membrane bound cell division protein at septum containing leucine zipper motif |
* | REL606 | 100,408 | 0 | T→G | 29.0% | 11.2 | 63 | 518 | murD | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑ glutamatesynthetase |
* | REL606 | 139,812 | 0 | G→T | 36.4% | 26.0 | 44 | intergenic (‑92/‑74) | yacC/cueO | hypothetical protein/multicopper oxidase (laccase) |
* | REL606 | 157,994 | 0 | G→T | 25.7% | 10.3 | 35 | 277 | htrE | predicted outer membrane usher protein |
* | REL606 | 165,669 | 0 | T→G | 29.8% | 12.1 | 47 | 714 | hrpB | predicted ATP‑dependent helicase |
* | REL606 | 260,181 | 0 | T→G | 28.1% | 12.0 | 64 | 27 | pepD | aminoacyl‑histidine dipeptidase (peptidase D) |
* | REL606 | 260,184 | 0 | A→G | 32.2% | 22.1 | 59 | 24 | pepD | aminoacyl‑histidine dipeptidase (peptidase D) |
* | REL606 | 398,445 | 0 | T→G | 16.7% | 10.1 | 48 | 518 | secF | protein export protein SecF |
* | REL606 | 402,056 | 0 | T→G | 33.3% | 12.5 | 66 | 180 | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
* | REL606 | 506,207 | 0 | T→G | 25.0% | 11.8 | 68 | 126 | gcl | glyoxylate carboligase |
* | REL606 | 583,805 | 0 | A→C | 32.5% | 12.6 | 41 | 944 | pheP | phenylalanine transporter |
* | REL606 | 642,517 | 0 | T→G | 25.0% | 10.5 | 56 | 283 | lipA | lipoyl synthase |
* | REL606 | 676,263 | 0 | T→G | 24.7% | 13.0 | 73 | 788 | yleA | isopentenyl‑adenosine A37 tRNA methylthiolase |
* | REL606 | 869,821 | 0 | A→G | 30.4% | 11.5 | 56 | 767 | yliG | predicted SAM‑dependent methyltransferase |
* | REL606 | 964,805 | 0 | A→G | 27.4% | 14.9 | 63 | 484 | ycaM | predicted transporter |
* | REL606 | 986,054 | 0 | T→G | 33.3% | 10.4 | 31 | 597 | lpxK | tetraacyldisaccharide 4'‑kinase |
* | REL606 | 987,456 | 0 | G→T | 24.5% | 12.2 | 49 | 976 | ycaQ | hypothetical protein |
* | REL606 | 1,029,241 | 0 | T→C | 20.7% | 11.5 | 58 | 150 | pqiA | paraquat‑inducible membrane protein A |
* | REL606 | 1,029,245 | 0 | A→C | 32.1% | 13.8 | 57 | 154 | pqiA | paraquat‑inducible membrane protein A |
* | REL606 | 1,117,181 | 0 | G→T | 30.8% | 11.9 | 40 | 585 | csgD | DNA‑binding transcriptional activator in two‑component regulatory system |
* | REL606 | 1,168,136 | 0 | C→G | 27.8% | 10.5 | 36 | 268 | pabC | 4‑amino‑4‑deoxychorismate lyase |
* | REL606 | 1,242,906 | 0 | T→G | 27.9% | 10.8 | 61 | 325 | ldcA | L,D‑carboxypeptidase A |
* | REL606 | 1,318,108 | 0 | T→G | 37.5% | 10.2 | 24 | 871 | trpD | bifunctional indole‑3‑glycerol‑phosphate synthase/anthranilate phosphoribosyltransferase |
* | REL606 | 1,509,936 | 0 | A→G | 40.0% | 18.9 | 40 | pseudogene (74/567 nt) | yddE | hypothetical protein; b1464_2 |
* | REL606 | 1,536,774 | 0 | G→T | 28.8% | 16.5 | 60 | 241 | ddpX | D‑ala‑D‑ala dipeptidase, Zn‑dependent |
* | REL606 | 1,538,235 | 0 | G→T | 25.9% | 11.9 | 54 | 1437 | dos | cAMP phosphodiesterase, heme‑regulated |
* | REL606 | 1,595,111 | 0 | T→G | 25.4% | 18.2 | 55 | 36 | dcp | dipeptidyl carboxypeptidase II |
* | REL606 | 1,714,634 | 0 | T→A | 19.5% | 13.1 | 42 | intergenic (‑77/+89) | ydhP/ECB_01628 | putative transport protein (MFS family); b1657_2/predicted transporter |
* | REL606 | 1,714,640 | 0 | T→A | 17.5% | 10.6 | 43 | intergenic (‑83/+83) | ydhP/ECB_01628 | putative transport protein (MFS family); b1657_2/predicted transporter |
* | REL606 | 1,812,720 | 0 | G→T | 33.3% | 11.1 | 27 | 685 | ydjZ | conserved inner membrane protein |
* | REL606 | 1,854,385 | 0 | C→G | 34.9% | 19.6 | 43 | 248 | yeaO | hypothetical protein |
* | REL606 | 1,854,388 | 0 | A→G | 33.3% | 12.3 | 39 | 251 | yeaO | hypothetical protein |
* | REL606 | 2,006,294 | 0 | A→C | 23.3% | 13.9 | 60 | 365 | insD | IS2 insertion element transposase InsAB' |
* | REL606 | 2,056,849 | 0 | T→G | 28.6% | 10.9 | 49 | 877 | cpsB | mannose‑1‑phosphate guanyltransferase |
* | REL606 | 2,167,569 | 0 | T→G | 35.7% | 10.9 | 43 | 105 | yehW | predicted transporter subunit: membrane component of ABC superfamily |
* | REL606 | 2,197,867 | 0 | T→G | 28.3% | 11.4 | 60 | 141 | cirA | ferric iron‑catecholate outer membrane transporter |
* | REL606 | 2,233,519 | 0 | T→G | 31.5% | 10.6 | 56 | 1700 | yejH | predicted ATP‑dependet helicase |
* | REL606 | 2,304,369 | 0 | A→G | 29.5% | 11.5 | 61 | 758 | yfaD | hypothetical protein |
* | REL606 | 2,402,889 | 0 | T→C | 33.3% | 12.0 | 39 | 1245 | yfcY | acetyl‑CoA acetyltransferase |
* | REL606 | 2,433,454 | 0 | A→T | 19.7% | 13.2 | 61 | 559 | ypdA | predicted sensory kinase in two‑component system with YpdB |
* | REL606 | 2,501,962 | 0 | T→G | 25.0% | 11.2 | 40 | 1499 | tktB | transketolase 2, thiamin‑binding |
* | REL606 | 2,698,093 | 0 | T→. | 66.7% | 54.3 | 36 | coding (1994/2145 nt) | nrdE | ribonucleotide‑diphosphate reductase alpha subunit |
* | REL606 | 3,000,240 | 0 | C→G | 20.8% | 12.0 | 48 | 677 | flu | antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
* | REL606 | 3,037,598 | 0 | A→C | 31.6% | 10.5 | 38 | 1397 | ECB_02838 | GspD, hypothetical type II secretion protein |
* | REL606 | 3,176,131 | 0 | T→C | 28.8% | 11.0 | 52 | 218 | uxaA | altronate hydrolase |
* | REL606 | 3,218,962 | 0 | A→G | 27.9% | 10.5 | 43 | 587 | agaY | tagatose 6‑phosphate aldolase 1, kbaY subunit |
* | REL606 | 3,268,991 | 0 | T→G | 28.2% | 18.4 | 39 | 48 | ispB | octaprenyl diphosphate synthase |
* | REL606 | 3,279,786 | 0 | T→G | 31.4% | 10.1 | 53 | 608 | yhbG | predicted transporter subunit: ATP‑binding component of ABC superfamily |
* | REL606 | 3,289,196 | 0 | A→C | 32.4% | 13.0 | 37 | 90 | yhcC | predicted Fe‑S oxidoreductase |
* | REL606 | 3,356,999 | 0 | G→T | 31.6% | 78.5 | 165 | intergenic (‑332/‑142) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
* | REL606 | 3,357,000 | 0 | A→T | 56.1% | 104.3 | 163 | intergenic (‑333/‑141) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
* | REL606 | 3,357,002 | 0 | C→T | 49.0% | 161.6 | 162 | intergenic (‑335/‑139) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
* | REL606 | 3,357,010 | 0 | C→T | 53.5% | 117.6 | 161 | intergenic (‑343/‑131) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
* | REL606 | 3,357,012 | 0 | G→T | 62.3% | 81.0 | 151 | intergenic (‑345/‑129) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
* | REL606 | 3,357,016 | 0 | G→T | 63.3% | 94.6 | 146 | intergenic (‑349/‑125) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
* | REL606 | 3,357,019 | 0 | G→T | 65.7% | 92.2 | 154 | intergenic (‑352/‑122) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
* | REL606 | 3,361,473 | 0 | T→C | 26.0% | 11.6 | 50 | intergenic (‑8/‑122) | smf/def | hypothetical protein/peptide deformylase |
* | REL606 | 3,369,868 | 0 | T→G | 26.7% | 10.4 | 30 | 136 | rpsK | 30S ribosomal protein S11 |
* | REL606 | 3,424,862 | 0 | A→T | 30.9% | 20.7 | 44 | intergenic (+80/‑46) | nirD/nirC | nitrite reductase small subunit/nitrite transporter |
* | REL606 | 3,424,863 | 0 | A→T | 27.9% | 13.2 | 44 | intergenic (+81/‑45) | nirD/nirC | nitrite reductase small subunit/nitrite transporter |
* | REL606 | 3,424,870 | 0 | G→T | 25.0% | 11.4 | 41 | intergenic (+88/‑38) | nirD/nirC | nitrite reductase small subunit/nitrite transporter |
* | REL606 | 3,424,875 | 0 | A→T | 27.5% | 18.4 | 45 | intergenic (+93/‑33) | nirD/nirC | nitrite reductase small subunit/nitrite transporter |
* | REL606 | 3,424,882 | 0 | G→T | 29.2% | 23.9 | 49 | intergenic (+100/‑26) | nirD/nirC | nitrite reductase small subunit/nitrite transporter |
* | REL606 | 3,450,872 | 0 | A→C | 23.8% | 11.3 | 42 | 562 | yrfD | predicted pilus assembly protein |
* | REL606 | 3,535,035 | 0 | T→C | 26.9% | 11.1 | 52 | intergenic (‑104/‑46) | ftsY/yhhF | fused Signal Recognition Particle (SRP) receptor: membrane binding protein/conserved protein/predicted methyltransferase |
* | REL606 | 3,560,696 | 0 | G→T | 18.6% | 11.9 | 61 | 595 | yhiI | predicted HlyD family secretion protein |
* | REL606 | 3,577,411 | 0 | T→G | 32.3% | 13.3 | 31 | 423 | gor | glutathione reductase |
* | REL606 | 3,610,860 | 0 | A→G | 17.9% | 10.4 | 78 | 573 | yhjJ | predicted zinc‑dependent peptidase |
* | REL606 | 3,671,974 | 0 | C→A | 23.6% | 18.4 | 55 | 65 | yiaI | predicted hydrogenase, 4Fe‑4S ferredoxin‑type component |
* | REL606 | 3,758,626 | 0 | A→C | 32.6% | 15.0 | 43 | 902 | yicF | NAD‑dependent DNA ligase LigB |
* | REL606 | 3,781,657 | 0 | G→T | 31.1% | 15.0 | 45 | 322 | ECB_03521 | conserved hypothetical protein |
* | REL606 | 3,977,993 | 0 | A→G | 27.1% | 15.7 | 60 | 514 | metE | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine methyltransferase |
* | REL606 | 4,080,986 | 0 | T→G | 41.7% | 10.3 | 25 | intergenic (+74/‑186) | sodA/kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxygluconate permease |
* | REL606 | 4,126,083 | 0 | T→G | 21.4% | 12.7 | 58 | 1982 | pflD | predicted formate acetyltransferase 2 (pyruvate formate lyase II) |
* | REL606 | 4,320,382 | 0 | A→G | 33.3% | 11.0 | 36 | intergenic (‑40/‑243) | melR/melA | DNA‑binding transcriptional dual regulator/alpha‑galactosidase, NAD(P)‑binding |
* | REL606 | 4,462,991 | 0 | A→T | 61.1% | 119.0 | 207 | 229 | yjgN | conserved inner membrane protein |
* | REL606 | 4,462,992 | 0 | G→T | 33.0% | 133.5 | 209 | 230 | yjgN | conserved inner membrane protein |
* | REL606 | 4,462,995 | 0 | G→T | 42.1% | 163.9 | 212 | 233 | yjgN | conserved inner membrane protein |
* | REL606 | 4,462,997 | 0 | C→T | 54.0% | 171.4 | 214 | 235 | yjgN | conserved inner membrane protein |
* | REL606 | 4,463,000 | 0 | G→T | 42.0% | 175.0 | 198 | 238 | yjgN | conserved inner membrane protein |
* | REL606 | 4,463,006 | 0 | G→T | 51.7% | 204.0 | 198 | 244 | yjgN | conserved inner membrane protein |
* | REL606 | 4,463,014 | 0 | C→T | 38.4% | 104.0 | 130 | 252 | yjgN | conserved inner membrane protein |
* | REL606 | 4,463,016 | 0 | A→T | 49.1% | 144.4 | 116 | 254 | yjgN | conserved inner membrane protein |
* | REL606 | 4,488,100 | 0 | G→T | 28.0% | 12.7 | 51 | 922 | yjhC | predicted oxidoreductase |
* | REL606 | 4,520,373 | 0 | G→T | 29.6% | 11.0 | 54 | intergenic (‑734/‑722) | yjhA/fimB | N‑acetylnuraminic acid outer membrane channel protein/recombinase involved in phase variation; regulator for fimA; b4312_1 |
* | REL606 | 4,582,471 | 0 | T→G | 36.4% | 12.9 | 34 | 1580 | tsr | methyl‑accepting chemotaxis protein I, serine sensor receptor |
* | REL606 | 4,620,003 | 0 | C→G | 22.2% | 12.4 | 45 | 1058 | slt | lytic murein transglycosylase, soluble |
* | REL606 | 4,621,274 | 0 | A→G | 26.0% | 15.8 | 50 | 302 | trpR | Trp operon repressor |
* | REL606 | 4,628,027 | 0 | T→G | 25.9% | 11.3 | 58 | 440 | arcA | DNA‑binding response regulator in two‑component regulatory system with ArcB or CpxA |
Marginal new junction evidence... | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | REL606 | 809428 = | 43 (0.910) | 8 (0.170) | 6/60 | 4.4 | 16.0% | intergenic (‑155/‑242) | ybhK/moaA | predicted transferase with NAD(P)‑binding Rossmann‑fold domain/molybdenum cofactor biosynthesis protein A |
? | REL606 | = 4141016 | 41 (0.740) | coding (89/705 nt) | yijC | DNA‑binding transcriptional repressor | |||||
* | ? | REL606 | 1427340 = | 46 (0.890) | 6 (0.120) | 4/66 | 5.7 | 13.2% | intergenic (‑115/+26) | ynaF/ompN | stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific |
? | REL606 | 4022380 = | 33 (0.600) | intergenic (+39/‑116) | dsbA/yihF | periplasmic protein disulfide isomerase I/hypothetical protein | |||||
* | ? | REL606 | = 3749572 | 40 (0.880) | 8 (0.180) | 4/58 | 5.2 | 16.5% | intergenic (‑65/+33) | mutM/rpmG | formamidopyrimidine‑DNA glycosylase/50S ribosomal protein L33 |
? | REL606 | = 4157631 | 41 (0.740) | coding (278/546 nt) | nusG | transcription antitermination protein NusG | |||||
* | ? | REL606 | = 3813062 | 39 (0.850) | 8 (0.180) | 4/58 | 5.2 | 16.7% | intergenic (‑143/‑791) | ivbL/emrD | ilvB operon leader peptide/multidrug efflux system protein |
? | REL606 | = 4157631 | 41 (0.740) | coding (278/546 nt) | nusG | transcription antitermination protein NusG | |||||
* | ? | REL606 | 3944627 = | 36 (0.820) | 8 (0.180) | 4/56 | 5.1 | 17.0% | intergenic (+16/‑131) | proM/aslB | tRNA‑Pro/predicted regulator of arylsulfatase activity |
? | REL606 | = 4157630 | 42 (0.760) | coding (277/546 nt) | nusG | transcription antitermination protein NusG | |||||
* | ? | REL606 | 72407 = | 27 (0.610) | 4 (0.090) | 4/56 | 5.1 | 9.1% | coding (446/1701 nt) | araB | ribulokinase |
? | REL606 | 3650765 = | 53 (0.960) | intergenic (+46/+141) | cspA/hokA | major cold shock protein/toxic polypeptide, small | |||||
* | ? | REL606 | = 1440018 | 48 (1.170) | 3 (0.070) | 3/52 | 5.3 | 5.9% | coding (894/1500 nt) | feaB | phenylacetaldehyde dehydrogenase |
? | REL606 | = 4081044 | 47 (0.850) | intergenic (+132/‑128) | sodA/kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxygluconate permease | |||||
* | ? | REL606 | 2429311 = | 33 (0.780) | 4 (0.090) | 3/54 | 5.5 | 11.0% | coding (206/243 nt) | yfdY | predicted inner membrane protein |
? | REL606 | = 2792989 | 32 (0.580) | coding (481/849 nt) | ECB_02621 | conserved hypothetical protein |