mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 2,766 | G→A | 5.6% | L810L (CTG→CTA) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 83,590 | G→T | 5.3% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 280,618 | T→C | 5.8% | pseudogene (118/309 nt) | yagB ← | pseudogene, CP4‑6 prophage;Phage or Prophage Related |
| RA | 347,692 | C→A | 9.5% | G251V (GGC→GTC) | prpR ← | propionate catabolism operon regulatory protein |
| RA | 755,486 | G→T | 22.5% | E104* (GAA→TAA) | sdhC → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 756,061:1 | +C | 39.2% | coding (155/1767 nt) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| JC | 756,377 | Δ48 bp | 6.9% | coding (471‑518/1767 nt) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 756,606 | C→T | 12.1% | Q234* (CAG→TAG) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| JC | 757,282 | Δ69 bp | 10.9% | coding (1376‑1444/1767 nt) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 757,972:1 | +A | 7.2% | coding (284/717 nt) | sdhB → | succinate dehydrogenase, FeS subunit |
| RA | 757,972:2 | +G | 7.2% | coding (284/717 nt) | sdhB → | succinate dehydrogenase, FeS subunit |
| RA | 812,200 | C→G | 5.1% | Q227E (CAA→GAA) | bioC → | malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| RA | 1,057,709 | G→A | 5.5% | R82R (CGC→CGT) | torR ← | response regulator in two‑component regulatory system with TorS |
| RA | 1,240,641 | C→T | 6.0% | P477P (CCG→CCA) | cvrA ← | putative cation/proton antiporter |
| RA | 1,279,940 | T→A | 8.1% | L26H (CTC→CAC) | narG → | nitrate reductase 1, alpha subunit |
| RA | 1,287,024 | G→A | 9.4% | intergenic (+498/+42) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,287,143 | G→A | 6.5% | noncoding (94/171 nt) P12S (CCA→TCA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,287,152 | T→C | 8.4% | noncoding (85/171 nt) T9A (ACT→GCT) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,287,161 | G→A | 8.3% | noncoding (76/171 nt) Q6* (CAA→TAA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,449,473 | C→T | 5.6% | R626H (CGC→CAC) | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,466,336 | C→G | 6.8% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,345 | T→C | 6.0% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,472,951 | C→T | 5.0% | pseudogene (2435/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,553,553 | T→C | 6.1% | N96D (AAC→GAC) | adhP ← | ethanol‑active dehydrogenase/acetaldehyde‑active reductase |
| RA | 1,560,364 | A→G | 5.2% | L189P (CTG→CCG) | ddpB ← | D,D‑dipeptide ABC transporter permease |
| RA | 1,587,836 | C→A | 15.1% | G154V (GGA→GTA) | ydeR ← | putative fimbrial‑like adhesin protein |
| RA | 1,852,303 | C→A | 5.1% | R139R (CGC→CGA) | pncA → | nicotinamidase/pyrazinamidase |
| RA | 1,957,069 | A→C | 5.5% | F355C (TTC→TGC) | torY ← | TMAO reductase III (TorYZ), cytochrome c‑type subunit |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,030,947 | C→T | 6.8% | A457A (GCG→GCA) | dcm ← | DNA cytosine methyltransferase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,252,476 | T→A | 5.2% | N259K (AAT→AAA) | yeiI → | putative kinase |
| RA | 2,278,883 | G→T | 5.1% | A293E (GCA→GAA) | bcr ← | bicyclomycin/cysteine/sulfonamide efflux transporter |
| RA | 2,305,085 | A→G | 5.6% | intergenic (+692/+23) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,086 | C→G | 5.2% | intergenic (+693/+22) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,087 | C→T | 5.4% | intergenic (+694/+21) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,357,836 | G→A | 5.5% | pseudogene (33/198 nt) | ypaA → | pseudogene, C‑terminal fragment, Transposase_31 family |
| RA | 2,357,848 | A→G | 6.1% | pseudogene (45/198 nt) | ypaA → | pseudogene, C‑terminal fragment, Transposase_31 family |
| RA | 2,368,810 | A→T | 5.2% | S258C (AGC→TGC) | arnA → | fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase |
| RA | 2,378,333 | A→G | 5.9% | V309V (GTT→GTC) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| RA | 2,560,996 | G→T | 16.8% | intergenic (+98/‑372) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,695,037 | C→A | 5.3% | Q169H (CAG→CAT) | purL ← | phosphoribosylformyl‑glycineamide synthetase |
| RA | 2,852,543 | A→G | 5.1% | P136P (CCA→CCG) | hypD → | hydrogenase maturation protein |
| RA | 2,863,159 | A→G | 5.0% | P275P (CCA→CCG) | ygbK → | FliA‑regulated DUF1537 family protein |
| RA | 2,947,465 | Δ1 bp | 10.0% | intergenic (+2/‑32) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 3,140,844 | G→A | 6.2% | A148V (GCG→GTG) | hybD ← | maturation protease for hydrogenase 2 |
| RA | 3,269,967 | C→T | 5.0% | intergenic (+365/+249) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,269,969 | A→C | 7.0% | intergenic (+367/+247) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,269,970 | A→G | 5.1% | intergenic (+368/+246) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,392,260 | C→T | 5.8% | intergenic (‑232/+198) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,424,661 | C→A | 5.2% | noncoding (2123/2904 nt) | rrlD ← | 23S ribosomal RNA of rrnD operon |
| RA | 3,472,627 | G→A | 5.2% | N296N (AAC→AAT) | fusA ← | protein chain elongation factor EF‑G, GTP‑binding |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,683,472 | G→A | 5.0% | intergenic (‑25/+158) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| RA | 3,683,473 | G→A | 5.0% | intergenic (‑26/+157) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| RA | 3,683,479 | T→C | 6.0% | intergenic (‑32/+151) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| RA | 3,683,497 | G→A | 43.6% | intergenic (‑50/+133) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,882,476 | A→G | 5.7% | T418T (ACT→ACC) | dnaA ← | chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator |
| RA | 3,959,480 | A→T | 5.9% | intergenic (+35/+52) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,481 | C→G | 5.9% | intergenic (+36/+51) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,975,356 | Δ1 bp | 5.1% | coding (211/1131 nt) | wecE → | TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,224,845 | T→C | 5.2% | C340R (TGC→CGC) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 4,296,060 | C→T | 36.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,307,038 | G→A | 5.3% | F254F (TTC→TTT) | alsK ← | D‑allose kinase |
| JC JC | 4,504,598 | IS5 (–) +4 bp | 40.4% | coding (541‑544/1218 nt) | yjhB → | putative MFS transporter, membrane protein |
| RA | 4,549,932 | T→A | 5.6% | intergenic (+222/+21) | fimH → / ← gntP | minor component of type 1 fimbriae/fructuronate transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 761495 | 762756 | 1262 | 37 [34] | [36] 38 | [sucA]–sucB | [sucA],sucB |
| * | * | ÷ | NC_000913 | 3423762–3424234 | 3424544–3424238 | 5–783 | 37 [36] | [35] 37 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 274620 = | NA (NA) | 7 (0.070) | 6/238 | NT | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 7 (0.070) | 6/256 | NT | 5.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1196386 = | 116 (1.150) | intergenic (+13/+481) | icd/ymfD | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase/e14 prophage; putative SAM‑dependent methyltransferase | |||||
| * | ? | NC_000913 | 1207790 = | 24 (0.240) | 63 (0.710) | 52/224 | NT | 67.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 41 (0.460) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 26 (0.260) | 29 (0.330) | 28/224 | NT | 47.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 41 (0.460) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 157 (1.600) | 103/248 | NT | 99.7% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1411899 = | 111 (1.100) | 15 (0.190) | 13/204 | NT | 15.6% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 74 (0.920) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 4542690 | 172 (1.700) | 10 (0.110) | 10/238 | NT | 5.8% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 163 (1.740) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||