mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.20 revision c633c5005425
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Possible mixed read alignment sites... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | REL606 | 87,812 | 0 | T→G | 35.4% | 16.8 | 48 | V214G (GTT→GGT) | leuO | leucine transcriptional activator |
| * | REL606 | 92,359 | 0 | G→T | 25.6% | 14.5 | 39 | intergenic (+523/‑79) | fruR/yabB | DNA‑binding transcriptional dual regulator/hypothetical protein |
| * | REL606 | 93,946 | 0 | G→C | 34.0% | 13.4 | 48 | K37N (AAG→AAC) | ftsL | membrane bound cell division protein at septum containing leucine zipper motif |
| * | REL606 | 139,812 | 0 | G→T | 36.4% | 27.2 | 44 | intergenic (‑92/‑74) | yacC/cueO | hypothetical protein/multicopper oxidase (laccase) |
| * | REL606 | 165,669 | 0 | T→G | 30.4% | 11.6 | 46 | S238R (AGT→AGG) | hrpB | predicted ATP‑dependent helicase |
| * | REL606 | 260,181 | 0 | T→G | 27.0% | 10.8 | 63 | P9P (CCA→CCC) | pepD | aminoacyl‑histidine dipeptidase (peptidase D) |
| * | REL606 | 260,184 | 0 | A→G | 31.0% | 19.8 | 58 | S8S (TCT→TCC) | pepD | aminoacyl‑histidine dipeptidase (peptidase D) |
| * | REL606 | 342,345 | 0 | C→A | 22.2% | 10.1 | 55 | F393L (TTC→TTA) | mhpA | 3‑(3‑hydroxyphenyl)propionate hydroxylase |
| * | REL606 | 398,445 | 0 | T→G | 16.7% | 11.5 | 48 | V173G (GTG→GGG) | secF | protein export protein SecF |
| * | REL606 | 402,056 | 0 | T→G | 31.2% | 11.7 | 64 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | REL606 | 411,493 | 0 | T→C | 30.0% | 10.3 | 40 | M191V (ATT→GTT) | thiJ | hypothetical protein |
| * | REL606 | 506,207 | 0 | T→G | 25.4% | 11.9 | 67 | G42G (GGT→GGG) | gcl | glyoxylate carboligase |
| * | REL606 | 583,805 | 0 | A→C | 30.8% | 11.1 | 39 | N315T (AAC→ACC) | pheP | phenylalanine transporter |
| * | REL606 | 676,263 | 0 | T→G | 25.4% | 13.6 | 71 | H263P (CAC→CCC) | yleA | isopentenyl‑adenosine A37 tRNA methylthiolase |
| * | REL606 | 869,821 | 0 | A→G | 30.4% | 12.1 | 56 | I256T (ATC→ACC) | yliG | predicted SAM‑dependent methyltransferase |
| * | REL606 | 958,801 | 0 | T→G | 25.7% | 10.6 | 35 | G250G (GGT→GGG) | dmsA | dimethyl sulfoxide reductase, anaerobic, subunit A |
| * | REL606 | 964,805 | 0 | A→G | 25.0% | 13.0 | 61 | M162V (ATT→GTT) | ycaM | predicted transporter |
| * | REL606 | 1,117,181 | 0 | G→T | 30.8% | 12.4 | 40 | F195L (TTC→TTA) | csgD | DNA‑binding transcriptional activator in two‑component regulatory system |
| * | REL606 | 1,168,136 | 0 | C→G | 26.5% | 10.8 | 34 | R90G (CGA→GGA) | pabC | 4‑amino‑4‑deoxychorismate lyase |
| * | REL606 | 1,242,906 | 0 | T→G | 27.9% | 11.9 | 61 | T109P (ACC→CCC) | ldcA | L,D‑carboxypeptidase A |
| * | REL606 | 1,302,463 | 0 | T→G | 25.6% | 10.3 | 43 | V39G (GTC→GGC) | oppD | oligopeptide transporter ATP‑binding component |
| * | REL606 | 1,536,774 | 0 | G→T | 25.0% | 11.0 | 57 | Q81K (CAA→AAA) | ddpX | D‑ala‑D‑ala dipeptidase, Zn‑dependent |
| * | REL606 | 1,595,111 | 0 | T→G | 25.4% | 18.2 | 55 | T12T (ACA→ACC) | dcp | dipeptidyl carboxypeptidase II |
| * | REL606 | 1,854,385 | 0 | C→G | 30.8% | 11.7 | 39 | A83G (GCG→GGG) | yeaO | hypothetical protein |
| * | REL606 | 2,006,294 | 0 | A→C | 22.0% | 12.7 | 59 | V122G (GTG→GGG) | insD | IS2 insertion element transposase InsAB' |
| * | REL606 | 2,167,569 | 0 | T→G | 35.7% | 11.5 | 43 | Q35H (CAA→CAC) | yehW | predicted transporter subunit: membrane component of ABC superfamily |
| * | REL606 | 2,233,519 | 0 | T→G | 30.8% | 10.7 | 54 | V567G (GTG→GGG) | yejH | predicted ATP‑dependet helicase |
| * | REL606 | 2,304,369 | 0 | A→G | 28.3% | 10.6 | 60 | E253G (GAA→GGA) | yfaD | hypothetical protein |
| * | REL606 | 2,402,889 | 0 | T→C | 34.3% | 12.3 | 38 | G415G (GGA→GGG) | yfcY | acetyl‑CoA acetyltransferase |
| * | REL606 | 2,433,454 | 0 | A→T | 18.6% | 11.3 | 59 | M187F (ATT→TTT) | ypdA | predicted sensory kinase in two‑component system with YpdB |
| * | REL606 | 2,501,962 | 0 | T→G | 23.1% | 10.7 | 39 | V500G (GTG→GGG) | tktB | transketolase 2, thiamin‑binding |
| * | REL606 | 2,698,093 | 0 | T→. | 65.7% | 55.7 | 35 | coding (1994/2145 nt) | nrdE | ribonucleotide‑diphosphate reductase alpha subunit |
| * | REL606 | 3,000,240 | 0 | C→G | 19.1% | 11.0 | 47 | A226G (GCT→GGT) | flu | antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| * | REL606 | 3,176,131 | 0 | T→C | 29.4% | 11.3 | 51 | E73G (GAA→GGA) | uxaA | altronate hydrolase |
| * | REL606 | 3,268,991 | 0 | T→G | 28.2% | 19.1 | 39 | G16G (GGT→GGG) | ispB | octaprenyl diphosphate synthase |
| * | REL606 | 3,286,461 | 0 | T→G | 25.0% | 10.2 | 45 | L600F (TTA→TTC) | arcB | hybrid sensory histidine kinase in two‑component regulatory system with ArcA |
| * | REL606 | 3,357,002 | 0 | C→T | 24.4% | 16.6 | 47 | intergenic (‑335/‑139) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
| * | REL606 | 3,357,010 | 0 | C→T | 26.7% | 18.3 | 47 | intergenic (‑343/‑131) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
| * | REL606 | 3,357,012 | 0 | G→T | 28.6% | 10.2 | 37 | intergenic (‑345/‑129) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
| * | REL606 | 3,357,016 | 0 | G→T | 33.3% | 15.8 | 33 | intergenic (‑349/‑125) | rrsD/yrdA | 16S ribosomal RNA/hypothetical protein |
| * | REL606 | 3,361,473 | 0 | T→C | 26.0% | 12.1 | 50 | intergenic (‑8/‑122) | smf/def | hypothetical protein/peptide deformylase |
| * | REL606 | 3,535,035 | 0 | T→C | 27.5% | 10.7 | 51 | intergenic (‑104/‑46) | ftsY/yhhF | fused Signal Recognition Particle (SRP) receptor: membrane binding protein/conserved protein/predicted methyltransferase |
| * | REL606 | 3,610,860 | 0 | A→G | 17.9% | 11.3 | 78 | D191D (GAT→GAC) | yhjJ | predicted zinc‑dependent peptidase |
| * | REL606 | 3,640,845 | 0 | T→G | 40.0% | 10.2 | 31 | Y30S (TAC→TCC) | yhjW | predicted metal dependent hydrolase |
| * | REL606 | 3,671,974 | 0 | C→A | 22.2% | 17.2 | 54 | C22F (TGC→TTC) | yiaI | predicted hydrogenase, 4Fe‑4S ferredoxin‑type component |
| * | REL606 | 3,781,657 | 0 | G→T | 29.5% | 14.7 | 44 | E108* (GAA→TAA) | ECB_03521 | conserved hypothetical protein |
| * | REL606 | 3,943,011 | 0 | A→C | 25.7% | 10.2 | 35 | T109P (ACC→CCC) | yifK | predicted transporter |
| * | REL606 | 3,977,993 | 0 | A→G | 26.3% | 12.2 | 58 | K172E (AAA→GAA) | metE | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine methyltransferase |
| * | REL606 | 4,126,083 | 0 | T→G | 20.0% | 12.3 | 56 | V661G (GTA→GGA) | pflD | predicted formate acetyltransferase 2 (pyruvate formate lyase II) |
| * | REL606 | 4,462,991 | 0 | A→T | 52.4% | 126.4 | 152 | S77C (AGT→TGT) | yjgN | conserved inner membrane protein |
| * | REL606 | 4,462,992 | 0 | G→T | 33.8% | 100.1 | 154 | S77I (AGT→ATT) | yjgN | conserved inner membrane protein |
| * | REL606 | 4,462,995 | 0 | G→T | 38.9% | 113.0 | 157 | C78F (TGT→TTT) | yjgN | conserved inner membrane protein |
| * | REL606 | 4,462,997 | 0 | C→T | 51.1% | 146.7 | 159 | L79F (CTT→TTT) | yjgN | conserved inner membrane protein |
| * | REL606 | 4,463,000 | 0 | G→T | 46.3% | 142.9 | 143 | V80F (GTT→TTT) | yjgN | conserved inner membrane protein |
| * | REL606 | 4,463,006 | 0 | G→T | 43.9% | 141.8 | 143 | V82F (GTT→TTT) | yjgN | conserved inner membrane protein |
| * | REL606 | 4,463,014 | 0 | C→T | 44.4% | 116.8 | 127 | F84F (TTC→TTT) | yjgN | conserved inner membrane protein |
| * | REL606 | 4,463,016 | 0 | A→T | 49.5% | 139.8 | 112 | Y85F (TAT→TTT) | yjgN | conserved inner membrane protein |
| * | REL606 | 4,582,471 | 0 | T→G | 32.3% | 10.8 | 32 | V527G (GTG→GGG) | tsr | methyl‑accepting chemotaxis protein I, serine sensor receptor |
| * | REL606 | 4,621,274 | 0 | A→G | 26.5% | 15.8 | 49 | E101G (GAA→GGA) | trpR | Trp operon repressor |
| * | REL606 | 4,628,027 | 0 | T→G | 25.0% | 10.6 | 56 | N147T (AAC→ACC) | arcA | DNA‑binding response regulator in two‑component regulatory system with ArcB or CpxA |
| Marginal read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | REL606 | 3,351,171 | 0 | T→G | 100.0% | 3.5 | 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% | 1.8 | 2 | intergenic (‑156/+29) | rrlG/gltW | 23S ribosomal RNA/tRNA‑Glu |
| * | REL606 | 2,650,834 | 0 | C→A | 100.0% | 1.8 | 2 | intergenic (‑157/+28) | rrlG/gltW | 23S ribosomal RNA/tRNA‑Glu |
| * | REL606 | 569,034 | 0 | G→A | 100.0% | 1.7 | 2 | N301N (AAC→AAT) | yhhI | predicted transposase |
| * | REL606 | 569,036 | 0 | T→A | 100.0% | 1.7 | 2 | N301Y (AAC→TAC) | yhhI | predicted transposase |
| * | REL606 | 1,110,599 | 0 | G→A | 100.0% | 1.7 | 2 | G259G (GGC→GGT) | insF‑1 | putative transposase for IS3 |
| * | REL606 | 2,650,837 | 0 | C→T | 100.0% | 1.7 | 2 | intergenic (‑160/+25) | rrlG/gltW | 23S ribosomal RNA/tRNA‑Glu |
| * | REL606 | 2,842,128 | 0 | C→G | 100.0% | 1.6 | 3 | noncoding (13/77 nt) | metW | tRNA‑Met |
| * | REL606 | 2,650,839 | 0 | A→G | 100.0% | 1.5 | 2 | intergenic (‑162/+23) | rrlG/gltW | 23S ribosomal RNA/tRNA‑Glu |
| * | REL606 | 2,650,849 | 0 | A→T | 100.0% | 1.5 | 2 | intergenic (‑172/+13) | rrlG/gltW | 23S ribosomal RNA/tRNA‑Glu |
| * | REL606 | 569,294 | 0 | A→T | 100.0% | 1.4 | 2 | L215M (TTA→ATA) | yhhI | predicted transposase |
| * | REL606 | 3,354,702 | 0 | G→T | 100.0% | 1.4 | 2 | intergenic (‑23/+161) | rrlD/alaU | 23S ribosomal RNA/tRNA‑Ala |
| * | REL606 | 573,202 | 0 | T→G | 100.0% | 1.2 | 8 | H96P (CAC→CCC) | ECB_00530 | conserved hypothetical protein |
| * | REL606 | 1,110,603 | 0 | C→T | 100.0% | 1.1 | 2 | G258D (GGC→GAC) | insF‑1 | putative transposase for IS3 |
| * | REL606 | 1,607,946 | 0 | G→T | 100.0% | 1.0 | 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% | 0.9 | 2 | A294E (GCG→GAG) | gadB | glutamate decarboxylase B, PLP‑dependent |
| * | REL606 | 1,499,234 | 0 | A→G | 100.0% | 0.7 | 6 | E384G (GAG→GGG) | ECB_01413 | conserved hypothetical protein |
| * | REL606 | 2,055,806 | 0 | G→A | 100.0% | 0.7 | 1 | A97A (GCC→GCT) | cpsG | phosphomannomutase |
| * | 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% | 0.5 | 1 | E208G (GAA→GGA) | yhhI | predicted transposase |
| Marginal new junction evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | annotation | gene | product | ||
| * | ? | REL606 | = 1617633 | 44 (0.940) | 8 (0.170) | 6/60 | 4.4 | intergenic (+41/+115) | ECB_01527/ECB_01528 | putative lipoprotein/antitermination protein Q homolog from lambdoid prophage DLP12 |
| ? | REL606 | 4347927 = | 25 (0.460) | coding (1207/1257 nt) | yjeH | predicted transporter | ||||
| * | ? | REL606 | = 1619531 | 34 (0.780) | 10 (0.230) | 6/56 | 4.1 | intergenic (‑140/+77) | rem/hokD | predicted protein/small toxic polypeptide |
| ? | REL606 | 2353399 = | 35 (0.640) | coding (1545/1833 nt) | yfbS | predicted transporter | ||||
| * | ? | REL606 | = 3417473 | 65 (1.540) | 12 (0.280) | 6/54 | 3.9 | coding (613/1221 nt) | argD | bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase |
| ? | REL606 | = 4222576 | 45 (0.820) | coding (1432/1545 nt) | malF | maltose transporter subunit | ||||
| * | ? | REL606 | 1200603 = | 51 (1.050) | 8 (0.160) | 4/62 | 5.5 | coding (362/1137 nt) | potA | putrescine/spermidine ABC transporter ATPase protein |
| ? | REL606 | 2598461 = | 31 (0.570) | coding (600/1512 nt) | yphE | fused predicted sugar transporter subunits of ABC superfamily: ATP‑binding components | ||||
| * | ? | REL606 | 640118 = | 30 (0.620) | 9 (0.190) | 4/62 | 5.5 | intergenic (+36/+19) | cspE/ccrB | cold shock protein E/camphor resistance protein CrcB |
| ? | REL606 | 3198507 = | 44 (0.800) | coding (556/990 nt) | tdcB | threonine dehydratase | ||||
| * | ? | REL606 | 3882311 = | 61 (1.300) | 6 (0.130) | 4/60 | 5.3 | coding (107/816 nt) | atpB | F0F1 ATP synthase subunit A |
| ? | REL606 | 4418297 = | 53 (0.970) | coding (728/861 nt) | ytfG | NAD(P)H:quinone oxidoreductase | ||||
| * | ? | REL606 | 72407 = | 24 (0.510) | 6 (0.130) | 4/60 | 5.3 | coding (446/1701 nt) | araB | ribulokinase |
| ? | REL606 | 3944634 = | 38 (0.690) | intergenic (+23/‑124) | proM/aslB | tRNA‑Pro/predicted regulator of arylsulfatase activity | ||||
| * | ? | REL606 | 72407 = | 24 (0.510) | 5 (0.110) | 4/60 | 5.3 | coding (446/1701 nt) | araB | ribulokinase |
| ? | REL606 | 1286712 = | 49 (0.890) | intergenic (+36/‑147) | narI/ECB_01206 | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein | ||||
| * | ? | REL606 | = 339475 | 52 (1.510) | 5 (0.150) | 4/44 | 4.0 | coding (592/1083 nt) | lacI | lac repressor |
| ? | REL606 | = 2022999 | 50 (0.910) | coding (600/1071 nt) | hisC | histidinol‑phosphate aminotransferase | ||||
| * | ? | REL606 | = 2022999 | 50 (1.060) | 5 (0.110) | 4/60 | 5.3 | coding (600/1071 nt) | hisC | histidinol‑phosphate aminotransferase |
| ? | REL606 | = 2103918 | 22 (0.400) | coding (185/216 nt) | ECB_01992 | hypothetical protein | ||||