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 | 97,176 | G→C | 8.5% | V30V (GTG→GTC) | murD → | UDP‑N‑acetylmuramoyl‑L‑alanine‑‑D‑glutamate ligase |
| RA | 125,085 | T→A | 100% | I690N (ATC→AAC) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 282,518 | G→A | 7.3% | G81S (GGC→AGC) | yagE → | CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase |
| RA | 464,354 | C→A | 6.4% | intergenic (+46/‑48) | ybaV → / → fadM | helix‑hairpin‑helix 3 family protein/thioesterase III |
| RA | 464,356 | A→T | 6.1% | intergenic (+48/‑46) | ybaV → / → fadM | helix‑hairpin‑helix 3 family protein/thioesterase III |
| RA | 464,358 | T→G | 6.2% | intergenic (+50/‑44) | ybaV → / → fadM | helix‑hairpin‑helix 3 family protein/thioesterase III |
| RA | 551,570 | T→G | 7.6% | E342A (GAA→GCA) | purK ← | 5‑(carboxyamino)imidazole ribonucleotide synthase |
| JC JC | 568,268 | IS1 (–) +9 bp | 100% | intergenic (+21/‑39) | renD → / → emrE | DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE |
| RA | 603,393 | T→A | 8.6% | intergenic (+58/+23) | pheP → / ← ybdG | phenylalanine:H(+) symporter PheP/miniconductance mechanosensitive channel YbdG |
| RA | 685,056 | T→C | 8.9% | D67G (GAC→GGC) | gltL ← | glutamate/aspartate ABC transporter ATP binding subunit |
| RA | 857,576 | T→C | 12.1% | intergenic (+21/+220) | ybiT → / ← ybiU | ABC transporter ATP‑binding protein YbiT/DUF1479 domain‑containing protein YbiU |
| RA | 857,578 | C→G | 10.6% | intergenic (+23/+218) | ybiT → / ← ybiU | ABC transporter ATP‑binding protein YbiT/DUF1479 domain‑containing protein YbiU |
| RA | 857,580 | G→A | 9.0% | intergenic (+25/+216) | ybiT → / ← ybiU | ABC transporter ATP‑binding protein YbiT/DUF1479 domain‑containing protein YbiU |
| RA | 1,196,220 | C→T | 100% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,224,239 | A→T | 7.1% | intergenic (+332/+40) | ycgI → / ← minE | protein YcgI/Z‑ring positioning protein MinE |
| RA | 1,224,242 | A→T | 7.2% | intergenic (+335/+37) | ycgI → / ← minE | protein YcgI/Z‑ring positioning protein MinE |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| RA | 1,446,357:1 | +T | 7.5% | intergenic (+151/+21) | ydbL → / ← feaR | DUF1318 domain‑containing protein YdbL/DNA‑binding transcriptional activator FeaR |
| RA | 1,446,362 | Δ1 bp | 7.6% | intergenic (+156/+16) | ydbL → / ← feaR | DUF1318 domain‑containing protein YdbL/DNA‑binding transcriptional activator FeaR |
| RA | 1,666,468 | A→T | 6.5% | Q385L (CAG→CTG) | clcB → | putative chloride:H(+) antiporter ClcB |
| RA | 1,829,322 | A→C | 7.5% | L138R (CTG→CGG) | astD ← | aldehyde dehydrogenase |
| RA | 1,872,791 | A→G | 7.4% | T251A (ACT→GCT) | dgcJ → | putative diguanylate cyclase DgcJ |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,081,688 | A→T | 10.8% | I287N (ATT→AAT) | dacD ← | D‑alanyl‑D‑alanine carboxypeptidase DacD |
| RA | 2,090,122 | A→G | 9.2% | intergenic (+76/‑70) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,090,124 | C→G | 9.0% | intergenic (+78/‑68) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,090,126 | C→T | 10.6% | intergenic (+80/‑66) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,214,600 | G→A | 6.6% | C15C (TGC→TGT) | btsS ← | high‑affinity pyruvate receptor |
| RA | 2,521,344 | C→T | 11.4% | intergenic (+16/+249) | lysV → / ← xapR | tRNA‑Lys/DNA‑binding transcriptional activator XapR |
| RA | 2,521,346 | A→T | 11.6% | intergenic (+18/+247) | lysV → / ← xapR | tRNA‑Lys/DNA‑binding transcriptional activator XapR |
| RA | 2,521,348 | A→G | 11.9% | intergenic (+20/+245) | lysV → / ← xapR | tRNA‑Lys/DNA‑binding transcriptional activator XapR |
| RA | 2,536,370 | C→G | 11.3% | intergenic (+27/+16) | crr → / ← pdxK | Enzyme IIA(Glc)/pyridoxal kinase I |
| RA | 2,859,332 | T→G | 9.3% | L747R (CTC→CGC) | mutS → | DNA mismatch repair protein MutS |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| RA | 3,060,651 | T→C | 7.1% | intergenic (+5/‑199) | argP → / → scpA | DNA‑binding transcriptional dual regulator ArgP/methylmalonyl‑CoA mutase |
| RA | 3,183,345:1 | +T | 6.6% | intergenic (+22/+36) | zupT → / ← yqiD | heavy metal divalent cation transporter ZupT/protein YqiD |
| RA | 3,183,350 | Δ1 bp | 6.3% | intergenic (+27/+31) | zupT → / ← yqiD | heavy metal divalent cation transporter ZupT/protein YqiD |
| RA | 3,218,961 | T→A | 9.9% | Q39L (CAG→CTG) | aer ← | aerotaxis sensor receptor, flavoprotein |
| RA | 3,439,588 | G→C | 7.5% | intergenic (‑79/+28) | yhdN ← / ← rplQ | conserved protein YhdN/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 8.2% | intergenic (‑80/+27) | yhdN ← / ← rplQ | conserved protein YhdN/50S ribosomal subunit protein L17 |
| RA | 3,486,217 | A→C | 9.2% | Q33P (CAG→CCG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,556,609 | C→T | 8.3% | G81S (GGC→AGC) | rtcA ← | RNA 3'‑terminal phosphate cyclase |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,733,600 | A→G | 7.3% | E467G (GAA→GGA) | xylG → | xylose ABC transporter ATP binding subunit |
| RA | 3,810,321 | T→C | 7.0% | intergenic (+17/+22) | coaD → / ← mutM | pantetheine‑phosphate adenylyltransferase/DNA‑formamidopyrimidine glycosylase |
| RA | 3,810,324 | G→A | 5.7% | intergenic (+20/+19) | coaD → / ← mutM | pantetheine‑phosphate adenylyltransferase/DNA‑formamidopyrimidine glycosylase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,859,929 | C→T | 5.3% | G63D (GGC→GAC) | yidK ← | putative transporter YidK |
| RA | 3,900,410 | A→T | 6.6% | P56P (CCT→CCA) | yieL ← | putative hydrolase YieL |
| RA | 3,900,542 | A→T | 7.4% | I12I (ATT→ATA) | yieL ← | putative hydrolase YieL |
| RA | 3,900,545 | A→T | 7.5% | A11A (GCT→GCA) | yieL ← | putative hydrolase YieL |
| RA | 3,973,233 | T→G | 13.9% | C238G (TGC→GGC) | rffG → | dTDP‑glucose 4,6‑dehydratase 2 |
| RA | 3,976,399 | C→A | 5.1% | A41E (GCA→GAA) | wzxE → | lipid III flippase |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,138,006 | T→G | 5.2% | T344P (ACG→CCG) | gldA ← | L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase |
| RA | 4,138,011 | C→A | 5.2% | G342V (GGC→GTC) | gldA ← | L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,270,144 | G→C | 5.5% | intergenic (+17/‑94) | aphA → / → yjbQ | acid phosphatase/phosphotransferase/UPF0047 protein YjbQ |
| RA | 4,270,146 | T→C | 5.1% | intergenic (+19/‑92) | aphA → / → yjbQ | acid phosphatase/phosphotransferase/UPF0047 protein YjbQ |
| RA | 4,274,740 | G→A | 5.0% | intergenic (+79/+20) | ssb → / ← yjcB | ssDNA‑binding protein/uncharacterized protein YjcB |
| RA | 4,296,060 | C→T | 31.1% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,362,529 | T→C | 5.9% | intergenic (‑595/+22) | cadC ← / ← pheU | DNA‑binding transcriptional activator CadC/tRNA‑Phe |
| RA | 4,472,434 | G→A | 5.5% | R34* (CGA→TGA) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,472,437 | T→C | 6.2% | N33D (AAT→GAT) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,479,016 | G→C | 5.1% | intergenic (+127/+18) | rraB → / ← yjgM | ribonuclease E inhibitor protein B/putative acetyltransferase YjgM |
| RA | 4,549,932 | T→A | 5.8% | intergenic (+222/+21) | fimH → / ← gntP | type 1 fimbriae D‑mannose specific adhesin/fructuronate transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196230 | 1211461 | 15232 | 22 [19] | [20] 21 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3621183–3622298 | 3653144–3652030 | 29733–31962 | 23 [20] | [20] 21 | [rhsB]–[insH‑11] | [rhsB],yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,[insH‑11] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 46077 | 35 (0.640) | 3 (0.060) | 3/250 | NT | 8.0% | coding (271/1332 nt) | yaaU | putative transporter YaaU |
| ? | NC_000913 | = 46089 | 36 (0.690) | coding (283/1332 nt) | yaaU | putative transporter YaaU | |||||
| * | ? | NC_000913 | 225154 = | NA (NA) | 4 (0.080) | 4/254 | NT | NA | noncoding (1384/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | 225176 = | NA (NA) | noncoding (1406/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 710913 | NA (NA) | 3 (0.060) | 3/244 | NT | NA | noncoding (29/33 nt) | other | REP64 |
| ? | NC_000913 | = 710917 | NA (NA) | noncoding (25/33 nt) | other | REP64 | |||||
| * | ? | NC_000913 | = 932414 | 40 (0.730) | 4 (0.080) | 4/250 | NT | 9.3% | intergenic (‑364/‑181) | trxB/lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| ? | NC_000913 | = 932420 | 40 (0.770) | intergenic (‑370/‑175) | trxB/lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 66 (1.240) | 55/256 | NT | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1514036 | 33 (0.600) | 3 (0.060) | 3/250 | NT | 8.2% | coding (206/942 nt) | ydcU | putative ABC transporter membrane subunit YdcU |
| ? | NC_000913 | = 1514069 | 36 (0.690) | coding (239/942 nt) | ydcU | putative ABC transporter membrane subunit YdcU | |||||
| * | ? | NC_000913 | = 1598588 | 44 (0.800) | 3 (0.060) | 3/248 | NT | 6.9% | intergenic (‑502/+29) | yneO/lsrK | AIDA‑I family autotransporter YneO/autoinducer‑2 kinase |
| ? | NC_000913 | = 1598600 | 40 (0.780) | intergenic (‑514/+17) | yneO/lsrK | AIDA‑I family autotransporter YneO/autoinducer‑2 kinase | |||||
| * | ? | NC_000913 | 2042116 = | 42 (0.770) | 3 (0.060) | 3/244 | NT | 7.4% | intergenic (+91/‑252) | zinT/yodB | metal‑binding protein ZinT/putative cytochrome |
| ? | NC_000913 | 2042149 = | 36 (0.710) | intergenic (+124/‑219) | zinT/yodB | metal‑binding protein ZinT/putative cytochrome | |||||
| * | ? | NC_000913 | 2455052 = | 49 (0.890) | 4 (0.080) | 4/246 | NT | 8.0% | intergenic (‑51/+31) | yfcU/yfcV | putative outer membrane usher protein YfcU/putative fimbrial protein YfcV |
| ? | NC_000913 | 2455076 = | 46 (0.900) | intergenic (‑75/+7) | yfcU/yfcV | putative outer membrane usher protein YfcU/putative fimbrial protein YfcV | |||||
| * | ? | NC_000913 | 2848667 = | 29 (0.530) | 3 (0.060) | 3/258 | NT | 8.8% | coding (575/1827 nt) | hycC | formate hydrogenlyase subunit HycC |
| ? | NC_000913 | 2848734 = | 34 (0.630) | coding (508/1827 nt) | hycC | formate hydrogenlyase subunit HycC | |||||
| * | ? | NC_000913 | 3028494 = | 49 (0.890) | 4 (0.080) | 4/246 | NT | 8.4% | intergenic (+6/+30) | ghxQ/ygfS | guanine/hypoxanthine transporter GhxQ/putative oxidoreductase, 4Fe‑4S ferredoxin‑type subunit |
| ? | NC_000913 | 3028518 = | 42 (0.820) | intergenic (+30/+6) | ghxQ/ygfS | guanine/hypoxanthine transporter GhxQ/putative oxidoreductase, 4Fe‑4S ferredoxin‑type subunit | |||||
| * | ? | NC_000913 | 3383284 = | 40 (0.730) | 3 (0.060) | 3/240 | NT | 7.7% | intergenic (+17/+46) | degS/mdh | serine endoprotease/malate dehydrogenase |
| ? | NC_000913 | 3383314 = | 36 (0.720) | intergenic (+47/+16) | degS/mdh | serine endoprotease/malate dehydrogenase | |||||
| * | ? | NC_000913 | = 3620220 | NA (NA) | 3 (0.060) | 3/252 | NT | 100% | coding (1029/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3620255 | 0 (0.000) | coding (1064/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 3910444 = | NA (NA) | 3 (0.060) | 3/254 | NT | NA | noncoding (1/35 nt) | other | REP284 |
| ? | NC_000913 | 3910473 = | NA (NA) | noncoding (30/35 nt) | other | REP284 | |||||
| * | ? | NC_000913 | 3947039 = | 84 (1.530) | 6 (0.120) | 5/246 | NT | 6.8% | intergenic (+7/+89) | trpT/hdfR | tRNA‑Trp/DNA‑binding transcriptional dual regulator HdfR |
| ? | NC_000913 | 3947061 = | 86 (1.680) | intergenic (+29/+67) | trpT/hdfR | tRNA‑Trp/DNA‑binding transcriptional dual regulator HdfR | |||||
| * | ? | NC_000913 | 4053578 = | NA (NA) | 3 (0.060) | 3/250 | NT | NA | noncoding (1/37 nt) | other | REP294b |
| ? | NC_000913 | 4053609 = | NA (NA) | noncoding (32/37 nt) | other | REP294b | |||||
| * | ? | NC_000913 | 4127953 = | NA (NA) | 3 (0.060) | 3/250 | NT | NA | noncoding (1/34 nt) | other | REP305a |
| ? | NC_000913 | 4127981 = | NA (NA) | noncoding (29/34 nt) | other | REP305a | |||||