mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 330,986 | A→G | 3.0% | E508E (GAA→GAG) | betT → | choline transporter of high affinity |
| RA | 349,740 | C→A | 3.0% | intergenic (+168/‑272) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 375,045 | G→A | 4.1% | intergenic (+164/‑414) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 708,336 | G→A | 3.5% | M1M (ATG→ATA) † | chiP → | chitoporin, uptake of chitosugars |
| RA | 727,053 | Δ1 bp | 3.0% | intergenic (‑17/+6) | kdpB ← / ← kdpA | potassium translocating ATPase, subunit B/potassium translocating ATPase, subunit A |
| RA | 727,054 | Δ1 bp | 2.9% | intergenic (‑18/+5) | kdpB ← / ← kdpA | potassium translocating ATPase, subunit B/potassium translocating ATPase, subunit A |
| RA | 1,145,977 | C→T | 2.6% | intergenic (+78/+34) | rluC → / ← yceF | 23S rRNA pseudouridine(955,2504,2580) synthase/m(7)GTP pyrophosphatase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,426,237 | A→G | 2.9% | intergenic (+155/‑217) | ydaY → / → tmpR | pseudogene, Rac prophage,Phage or Prophage Related/Rac prophage, pseudogene, tail protein family,Phage or Prophage Related, putative alpha helix protein |
| RA | 1,466,201 | T→C | 5.6% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,210 | G→A | 7.1% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,258 | G→C | 6.1% | pseudogene (867/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,270 | C→T | 4.7% | pseudogene (879/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,280 | A→C | 4.7% | pseudogene (889/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,585 | T→C | 10.7% | pseudogene (1194/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,713 | C→A | 4.5% | pseudogene (1322/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,708,901 | A→G | 8.5% | R661R (CGA→CGG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,286,429:1 | +A | 2.7% | pseudogene (2484/2525 nt) | yejO ← | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| RA | 2,304,678 | T→C | 8.4% | intergenic (+287/+428) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,796 | T→C | 13.1% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,011 | A→G | 3.3% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,316,563 | C→T | 32.4% | T130I (ACC→ATC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,320,327 | T→C | 2.5% | F96S (TTC→TCC) | atoS → | sensory histidine kinase in two‑component regulatory system with AtoC |
| RA | 2,517,472 | T→A | 2.5% | Y120F (TAT→TTT) | yfeA ← | putative diguanylate cyclase |
| JC | 2,521,358 | Δ156 bp | 2.5% | intergenic (+32/+78) | lysV → / ← xapR | tRNA‑Lys/transcriptional activator of xapAB |
| JC | 2,765,454 | (TATGGCAC)6→5 | 2.9% | intergenic (‑303/+50) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage, uncharacterized protein |
| RA | 2,976,994 | C→A | 9.3% | S133* (TCA→TAA) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 2,977,027 | T→A | 4.7% | I144N (ATC→AAC) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 2,977,090 | G→A | 10.8% | W165* (TGG→TAG) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 3,368,980 | G→C | 2.9% | intergenic (+28/+32) | yhcG → / ← yhcH | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily/DUF386 family protein, cupin superfamily |
| RA | 3,515,994 | A→T | 2.8% | intergenic (‑83/+24) | dam ← / ← damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring |
| JC | 3,523,584:1 | (ACA)2→3 | 5.6% | coding (716/2553 nt) | mrcA → | penicillin‑binding protein 1a, murein transglycosylase and transpeptidase |
| RA | 3,527,604 | Δ1 bp | 30.6% | coding (1138/2136 nt) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,527,947 | C→G | 3.9% | T494R (ACA→AGA) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,528,602 | Δ1 bp | 11.3% | coding (2136/2136 nt) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,556,348 | A→T | 3.0% | V167E (GTG→GAG) | rtcA ← | RNA 3'‑terminal phosphate cyclase |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,531 | A→T | 11.0% | H32L (CAT→CTT) | yidX → | putative lipoprotein |
| RA | 3,992,437 | T→G | 20.7% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 3,992,468 | Δ4 bp | 8.1% | coding (1317‑1320/2547 nt) | cyaA → | adenylate cyclase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,110,110 | A→G | 3.0% | N61S (AAT→AGT) | cdh → | CDP‑diacylglycerol phosphotidylhydrolase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,295,833 | T→C | 6.2% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,295,963 | A→G | 2.9% | intergenic (+170/+474) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,295,964 | A→C | 3.4% | intergenic (+171/+473) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,154 | T→C | 26.9% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 47.1% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 52.1% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,326,089 | T→G | 8.6% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,148 | T→C | 6.0% | intergenic (‑406/+252) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533685 | 2536446 | 2762 | 82 [81] | [79] 82 | ptsH–[pdxK] | ptsH, ptsI, crr, [pdxK] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 141 (0.870) | 92/518 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 447227 | 152 (0.930) | 5 (0.030) | 4/496 | NT | 3.2% | coding (479/891 nt) | cyoE | protoheme IX farnesyltransferase |
| ? | NC_000913 | = 447266 | 158 (1.010) | coding (440/891 nt) | cyoE | protoheme IX farnesyltransferase | |||||
| * | ? | NC_000913 | 724117 = | 108 (0.660) | 3 (0.020) | 3/514 | NT | 2.8% | coding (298/2685 nt) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| ? | NC_000913 | 724160 = | 104 (0.640) | coding (255/2685 nt) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein | |||||
| * | ? | NC_000913 | 1207790 = | 66 (0.410) | 76 (0.500) | 60/486 | NT | 55.7% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 59 (0.390) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 61 (0.370) | 93 (0.610) | 66/486 | NT | 61.5% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 59 (0.390) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 4 (0.020) | 149 (0.910) | 90/518 | NT | 97.4% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1457975 | 107 (0.660) | 4 (0.030) | 4/498 | NT | 3.7% | coding (479/768 nt) | paaF | 2,3‑dehydroadipyl‑CoA hydratase |
| ? | NC_000913 | = 1457986 | 106 (0.680) | coding (490/768 nt) | paaF | 2,3‑dehydroadipyl‑CoA hydratase | |||||
| * | ? | NC_000913 | = 1979269 | NA (NA) | 10 (0.060) | 8/516 | NT | 5.5% | intergenic (‑54/‑484) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 3527244 = | 171 (1.050) | coding (778/2136 nt) | yrfF | putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 120 (0.740) | 72/518 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 165 (1.010) | 86/518 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | = 2024339 | 175 (1.070) | 12 (0.070) | 12/518 | NT | 6.5% | coding (372/624 nt) | rcsA | transcriptional regulator of colanic acid capsular biosynthesis |
| ? | NC_000913 | 2025115 = | 172 (1.060) | coding (130/228 nt) | yodD | uncharacterized protein | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 52 (0.320) | 42/518 | NT | 35.6% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 3526447 = | 94 (0.580) | intergenic (‑300/‑20) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 85 (0.520) | 59/516 | NT | 48.4% | intergenic (‑31/+2) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| ? | NC_000913 | = 3526451 | 91 (0.560) | intergenic (‑304/‑16) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | 3140341 = | 162 (0.990) | 4 (0.030) | 4/502 | NT | 2.5% | coding (457/489 nt) | hybE | hydrogenase 2‑specific chaperone |
| ? | NC_000913 | 3140360 = | 152 (0.960) | coding (438/489 nt) | hybE | hydrogenase 2‑specific chaperone | |||||
| * | ? | NC_000913 | 3368968 = | 149 (0.910) | 4 (0.030) | 4/494 | NT | 2.9% | intergenic (+16/+44) | yhcG/yhcH | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily/DUF386 family protein, cupin superfamily |
| ? | NC_000913 | 3368993 = | 126 (0.810) | intergenic (+41/+19) | yhcG/yhcH | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily/DUF386 family protein, cupin superfamily | |||||
| * | ? | NC_000913 | 3515980 = | 179 (1.100) | 5 (0.030) | 5/500 | NT | 3.0% | intergenic (‑69/+38) | dam/damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring |
| ? | NC_000913 | 3516008 = | 146 (0.930) | intergenic (‑97/+10) | dam/damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring | |||||
| * | ? | NC_000913 | 3845530 = | 128 (0.790) | 78 (0.500) | 51/498 | NT | 35.9% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992759 | 155 (0.990) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 12 (0.090) | 8/440 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||