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 | 125,387 | C→T | 100% | Q791* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 288,813 | T→C | 9.8% | E117G (GAA→GGA) | xynR ← | CP4‑6 prophage; DNA‑binding transcriptional repressor XynR |
| RA | 543,094 | G→C | 7.4% | intergenic (+61/+167) | glxK → / ← allE | glycerate 2‑kinase 2/(S)‑ureidoglycine aminohydrolase |
| RA | 563,871 | C→T | 10.5% | A204T (GCC→ACC) | fimZ ← | putative LuxR family transcriptional regulator FimZ |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 699,556 | C→T | 9.0% | intergenic (‑379/+18) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 699,559 | A→G | 8.2% | intergenic (‑382/+15) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 728,706 | G→A | 8.6% | I9I (ATC→ATT) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 759,250 | G→T | 100% | R182L (CGC→CTC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 800,807 | G→T | 100% | A17S (GCG→TCG) | ybhH → | putative isomerase YbhH |
| RA | 1,147,986 | G→C | 6.4% | L122L (CTG→CTC) | plsX → | putative phosphate acyltransferase |
| RA | 1,147,993 | A→C | 10.5% | I125L (ATT→CTT) | plsX → | putative phosphate acyltransferase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,466,345 | T→C | 17.2% | pseudogene (954/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,499,361 | A→G | 10.1% | N142D (AAC→GAC) | rimL → | ribosomal‑protein‑L12‑serine acetyltransferase |
| RA | 1,499,365 | A→T | 12.0% | Q143L (CAG→CTG) | rimL → | ribosomal‑protein‑L12‑serine acetyltransferase |
| RA | 1,499,369 | C→T | 10.2% | V144V (GTC→GTT) | rimL → | ribosomal‑protein‑L12‑serine acetyltransferase |
| RA | 1,657,593 | T→C | 8.9% | L10P (CTT→CCT) | ynfD → | DUF1161 domain‑containing protein YnfD |
| RA | 1,703,986 | T→A | 7.3% | D108V (GAT→GTT) | ydgJ ← | putative oxidoreductase YdgJ |
| 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 | 2,132,787 | 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 | 2,499,437 | T→A | 6.8% | V256D (GTT→GAT) | ypdA → | sensory histidine kinase YpdA |
| RA | 2,567,377 | A→G | 8.2% | V244A (GTG→GCG) | eutH ← | putative inner membrane protein |
| RA | 2,661,969 | C→G | 100% | V55L (GTT→CTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,897,018 | C→T | 9.1% | A285T (GCC→ACC) | ygcS ← | putative transporter YgcS |
| RA | 3,041,632 | T→A | 100% | V107E (GTG→GAG) | ygfZ → | folate‑binding protein |
| RA | 3,136,312 | C→A | 7.2% | L20L (CTG→CTT) | pitB ← | metal phosphate:H(+) symporter PitB |
| RA | 3,239,609 | T→G | 8.1% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator Alx/serine/threonine:Na(+) symporter |
| RA | 3,239,610 | C→G | 7.1% | intergenic (+65/‑334) | alx → / → sstT | putative membrane‑bound redox modulator Alx/serine/threonine:Na(+) symporter |
| RA | 3,253,285 | T→A | 7.3% | intergenic (+18/+33) | yhaI → / ← yhaJ | putative inner membrane protein/DNA‑binding transcriptional activator YhaJ |
| RA | 3,273,861 | C→T | 9.0% | L349L (CTG→CTA) | garP ← | galactarate/glucarate/glycerate transporter GarP |
| RA | 3,347,170 | G→A | 7.0% | R19H (CGT→CAT) | rapZ → | RNase adaptor protein |
| RA | 3,352,800 | C→A | 62.0% | V76F (GTC→TTC) | arcB ← | sensory histidine kinase ArcB |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,637,645:1 | +T | 100% | coding (4/1500 nt) | pitA → | metal phosphate:H(+) symporter PitA |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,030,911 | C→T | 8.4% | V21I (GTA→ATA) | fadB ← | dodecenoyl‑CoA delta‑isomerase, enoyl‑CoA hydratase, 3‑hydroxybutyryl‑CoA epimerase, 3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,114,431 | G→A | 100% | N14N (AAC→AAT) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,123,110 | G→A | 100% | P77L (CCA→CTA) | ftsN ← | cell division protein FtsN |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,189,827 | G→A | 6.8% | P14P (CCG→CCA) | yjaZ → | conserved protein YjaZ |
| RA | 4,268,494 | A→G | 9.2% | intergenic (+187/+315) | tyrB → / ← yjbS | tyrosine aminotransferase/uncharacterized protein YjbS |
| RA | 4,296,060 | C→T | 36.8% | 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 | 4,376,291 | T→C | 7.9% | intergenic (+26/‑26) | efp → / → ecnA | protein chain elongation factor EF‑P/entericidin A lipoprotein, antidote to entericidin B |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 239659 | 44 (0.850) | 3 (0.060) | 3/254 | NT | 6.5% | coding (531/771 nt) | yafV | 2‑oxoglutaramate amidase |
| ? | NC_000913 | = 239703 | 44 (0.880) | coding (487/771 nt) | yafV | 2‑oxoglutaramate amidase | |||||
| * | ? | NC_000913 | = 315572 | NA (NA) | 10 (0.210) | 7/242 | NT | NA | noncoding (344/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315588 | NA (NA) | noncoding (360/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315781 = | NA (NA) | 3 (0.060) | 3/252 | NT | NA | noncoding (553/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315875 = | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 316093 | NA (NA) | 4 (0.080) | 4/256 | NT | NA | noncoding (865/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316135 | NA (NA) | noncoding (907/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 316193 = | NA (NA) | 3 (0.060) | 3/244 | NT | NA | noncoding (965/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 316230 = | NA (NA) | noncoding (1002/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 2081 (40.730) | 250/260 | NT | 97.2% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 60 (1.170) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 572471 | 60 (1.170) | 9 (0.240) +34 bp |
7/194 | NT | 21.8% | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein |
| ? | NC_000913 | = 2170235 | 27 (0.520) | noncoding (65/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 758453 = | NA (NA) | 3 (0.060) | 3/248 | NT | NA | noncoding (1/34 nt) | other | REP67b |
| ? | NC_000913 | 758481 = | NA (NA) | noncoding (29/34 nt) | other | REP67b | |||||
| * | ? | NC_000913 | 1207790 = | 6 (0.120) | 41 (0.910) | 33/230 | NT | 85.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 9 (0.200) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 6 (0.120) | 27 (0.600) | 24/230 | NT | 79.1% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 9 (0.200) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1315791 = | 45 (0.870) | 4 (0.080) | 3/252 | NT | 8.9% | intergenic (‑21/+65) | yciF/yciG | DUF892 domain‑containing protein YciF/protein YciG |
| ? | NC_000913 | 1315813 = | 39 (0.790) | intergenic (‑43/+43) | yciF/yciG | DUF892 domain‑containing protein YciF/protein YciG | |||||
| * | ? | NC_000913 | 1426409 = | 53 (1.030) | 3 (0.060) | 3/246 | NT | 5.7% | intergenic (+429/‑45) | ydaY/ynaA | Rac prophage; putative uncharacterized protein YdaY/Rac prophage; putative prophage tail length tape measure domain‑containing protein YnaA |
| ? | NC_000913 | 1426431 = | 50 (1.030) | intergenic (+451/‑23) | ydaY/ynaA | Rac prophage; putative uncharacterized protein YdaY/Rac prophage; putative prophage tail length tape measure domain‑containing protein YnaA | |||||
| * | ? | NC_000913 | = 2533705 | 48 (0.930) | 3 (0.060) | 3/246 | NT | 6.2% | intergenic (+325/‑59) | cysK/ptsH | O‑acetylserine sulfhydrylase A/phosphocarrier protein HPr |
| ? | NC_000913 | = 2533719 | 45 (0.930) | intergenic (+339/‑45) | cysK/ptsH | O‑acetylserine sulfhydrylase A/phosphocarrier protein HPr | |||||
| * | ? | NC_000913 | 2664279 = | 47 (0.910) | 3 (0.060) | 3/252 | NT | 6.0% | intergenic (+34/‑111) | suhB/yfhR | inositol‑phosphate phosphatase/putative peptidase |
| ? | NC_000913 | 2664292 = | 48 (0.970) | intergenic (+47/‑98) | suhB/yfhR | inositol‑phosphate phosphatase/putative peptidase | |||||
| * | ? | NC_000913 | 3261397 = | 46 (0.890) | 3 (0.060) | 3/254 | NT | 6.4% | coding (1022/2295 nt) | tdcE | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 |
| ? | NC_000913 | 3261423 = | 43 (0.860) | coding (996/2295 nt) | tdcE | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 | |||||
| * | ? | NC_000913 | 3423665 = | NA (NA) | 5 (0.100) | 3/258 | NT | 9.4% | intergenic (‑10/+3) | thrV/rrfD | tRNA‑Thr/5S ribosomal RNA |
| ? | NC_000913 | = 4171803 | 49 (0.950) | intergenic (+47/‑254) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | 3493758 = | NA (NA) | 4 (0.080) | 4/246 | NT | NA | intergenic (+9/‑253) | tsgA/nirB | putative transporter TsgA/nitrite reductase catalytic subunit NirB |
| ? | NC_000913 | 3493784 = | NA (NA) | noncoding (26/26 nt) | other | REPt248 | |||||
| * | ? | NC_000913 | 3676120 = | NA (NA) | 4 (0.080) | 4/260 | NT | NA | intergenic (+12/+170) | yhjE/yhjG | putative transporter YhjE/AsmA family protein YhjG |
| ? | NC_000913 | 3676147 = | NA (NA) | noncoding (26/29 nt) | other | REPv264a | |||||
| * | ? | NC_000913 | 4020306 = | 61 (1.180) | 3 (0.060) | 3/254 | NT | 5.0% | coding (81/1641 nt) | ubiB | ubiquinone biosynthesis protein UbiB |
| ? | NC_000913 | 4020348 = | 54 (1.080) | coding (123/1641 nt) | ubiB | ubiquinone biosynthesis protein UbiB | |||||
| * | ? | NC_000913 | = 4040653 | 48 (0.930) | 3 (0.070) | 3/234 | NT | 5.9% | intergenic (+17/+253) | rrfA/mobB | 5S ribosomal RNA/molybdopterin‑guanine dinucleotide biosynthesis adaptor protein |
| ? | NC_000913 | = 4040669 | 52 (1.130) | intergenic (+33/+237) | rrfA/mobB | 5S ribosomal RNA/molybdopterin‑guanine dinucleotide biosynthesis adaptor protein | |||||
| * | ? | NC_000913 | = 4051966 | 60 (1.170) | 3 (0.060) | 3/254 | NT | 5.1% | intergenic (+110/‑79) | yihI/hemN | Der GTPase‑activating protein YihI/coproporphyrinogen III dehydrogenase |
| ? | NC_000913 | = 4052012 | 53 (1.060) | intergenic (+156/‑33) | yihI/hemN | Der GTPase‑activating protein YihI/coproporphyrinogen III dehydrogenase | |||||
| * | ? | NC_000913 | = 4099447 | 52 (1.010) | 3 (0.060) | 3/260 | NT | 5.4% | coding (802/849 nt) | rhaR | DNA‑binding transcriptional activator RhaR |
| ? | NC_000913 | = 4099475 | 53 (1.040) | coding (830/849 nt) | rhaR | DNA‑binding transcriptional activator RhaR | |||||
| * | ? | NC_000913 | = 4231923 | 41 (0.800) | 4 (0.080) | 3/256 | NT | 9.3% | coding (1311/1350 nt) | lysC | aspartate kinase III |
| ? | NC_000913 | = 4231939 | 38 (0.760) | coding (1295/1350 nt) | lysC | aspartate kinase III | |||||
| * | ? | NC_000913 | = 4545723 | 48 (0.930) | 3 (0.060) | 3/246 | NT | 6.1% | coding (628/2637 nt) | fimD | type I fimbriae usher protein |
| ? | NC_000913 | = 4545737 | 47 (0.970) | coding (642/2637 nt) | fimD | type I fimbriae usher protein | |||||