mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 76,805 | T→A | 100% | E165D (GAA→GAT) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 87,481 | C→A | 100% | T42K (ACA→AAA) | ilvH → | acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit |
| RA | 125,085 | Δ1 bp | 100% | coding (2069/2664 nt) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| JC JC | 568,268 | IS1 (–) +9 bp | 100% | intergenic (+21/‑39) | renD → / → emrE | DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE |
| RA | 781,668 | C→T | 7.6% | intergenic (+16/‑417) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase |
| RA | 781,670 | A→T | 9.1% | intergenic (+18/‑415) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase |
| RA | 781,672 | A→G | 7.7% | intergenic (+20/‑413) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase |
| RA | 1,196,220 | C→T | 100% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 100% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| 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 | 1,449,050 | T→A | 7.8% | intergenic (+32/+26) | feaB → / ← tynA | phenylacetaldehyde dehydrogenase/copper‑containing amine oxidase |
| RA | 1,638,039 | C→T | 10.3% | G24E (GGA→GAA) | ynfN ← | Qin prophage; protein YnfN |
| 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 | 2,416,622 | C→G | 100% | Q626E (CAG→GAG) | pta → | phosphate acetyltransferase |
| RA | 2,663,482 | A→C | 8.2% | K14T (AAG→ACG) | suhB → | inositol‑phosphate phosphatase |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| RA | 3,057,140 | A→G | 9.3% | intergenic (+149/+38) | sibC → / ← serA | small RNA SibC/phosphoglycerate dehydrogenase |
| RA | 3,057,145 | G→C | 9.4% | intergenic (+154/+33) | sibC → / ← serA | small RNA SibC/phosphoglycerate dehydrogenase |
| RA | 3,057,150 | C→T | 9.6% | intergenic (+159/+28) | sibC → / ← serA | small RNA SibC/phosphoglycerate dehydrogenase |
| RA | 3,176,209 | C→A | 100% | D209Y (GAT→TAT) | cpdA ← | cAMP phosphodiesterase |
| RA | 3,291,109 | A→T | 11.5% | K766* (AAA→TAA) ‡ | yraJ → | putative fimbrial usher protein YraJ |
| RA | 3,291,110 | A→T | 11.5% | K766I (AAA→ATA) ‡ | yraJ → | putative fimbrial usher protein YraJ |
| RA | 3,439,588 | G→C | 9.6% | intergenic (‑79/+28) | yhdN ← / ← rplQ | conserved protein YhdN/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 8.5% | intergenic (‑80/+27) | yhdN ← / ← rplQ | conserved protein YhdN/50S ribosomal subunit protein L17 |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,790,300 | A→T | 5.5% | intergenic (‑219/+20) | waaH ← / ← tdh | UDP‑glucuronate:LPS(HepIII) glycosyltransferase/threonine dehydrogenase |
| RA | 3,790,303 | A→T | 5.5% | intergenic (‑222/+17) | waaH ← / ← tdh | UDP‑glucuronate:LPS(HepIII) glycosyltransferase/threonine dehydrogenase |
| RA | 3,815,819 | C→G | 5.5% | intergenic (‑51/+44) | pyrE ← / ← rph | orotate phosphoribosyltransferase/truncated RNase PH |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,817,948 | G→T | 5.1% | E63D (GAG→GAT) | dinD → | DNA damage‑inducible protein D |
| RA | 3,817,949 | A→C | 5.2% | I64L (ATC→CTC) | dinD → | DNA damage‑inducible protein D |
| RA | 3,917,405 | A→T | 18.6% | V287V (GTT→GTA) | atpG ← | ATP synthase F1 complex subunit gamma |
| RA | 3,917,418 | C→A | 16.1% | G283V (GGG→GTG) | atpG ← | ATP synthase F1 complex subunit gamma |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,060,261 | G→T | 6.0% | intergenic (+31/‑186) | bipA → / → yihL | ribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL |
| RA | 4,060,264 | A→C | 6.3% | intergenic (+34/‑183) | bipA → / → yihL | ribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL |
| RA | 4,088,091 | G→C | 5.8% | intergenic (+34/+16) | yiiG → / ← frvR | DUF3829 domain‑containing lipoprotein YiiG/putative transcriptional regulator FrvR |
| RA | 4,113,473 | T→C | 6.4% | L61L (TTG→CTG) ‡ | uspD → | universal stress protein D |
| RA | 4,113,474 | T→A | 8.7% | L61* (TTG→TAG) ‡ | uspD → | universal stress protein D |
| RA | 4,113,475 | G→A | 7.3% | L61L (TTG→TTA) ‡ | uspD → | universal stress protein D |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,247,906 | C→A | 5.9% | intergenic (+7/‑65) | malK → / → lamB | maltose ABC transporter ATP binding subunit/maltose outer membrane channel/phage lambda receptor protein |
| RA | 4,270,142 | G→A | 5.8% | intergenic (+15/‑96) | aphA → / → yjbQ | acid phosphatase/phosphotransferase/UPF0047 protein YjbQ |
| RA | 4,270,144 | G→C | 6.9% | intergenic (+17/‑94) | aphA → / → yjbQ | acid phosphatase/phosphotransferase/UPF0047 protein YjbQ |
| RA | 4,270,146 | T→C | 6.1% | intergenic (+19/‑92) | aphA → / → yjbQ | acid phosphatase/phosphotransferase/UPF0047 protein YjbQ |
| RA | 4,296,060 | C→T | 26.3% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,155 | T→C | 19.2% | intergenic (+361/+281) | 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 | 4,323,426 | T→C | 11.2% | K309K (AAA→AAG) | phnD ← | phosphonate ABC transporter periplasmic binding protein |
| RA | 4,332,871 | A→C | 6.2% | S134R (AGT→AGG) | basS ← | sensory histidine kinase BasS |
| RA | 4,377,792 | A→T | 5.4% | intergenic (‑70/+19) | blc ← / ← ampC | outer membrane lipoprotein Blc/beta‑lactamase |
| RA | 4,479,012 | A→T | 6.7% | intergenic (+123/+22) | rraB → / ← yjgM | ribonuclease E inhibitor protein B/putative acetyltransferase YjgM |
| RA | 4,479,016 | G→C | 6.6% | intergenic (+127/+18) | rraB → / ← yjgM | ribonuclease E inhibitor protein B/putative acetyltransferase YjgM |
| RA | 4,479,020 | A→T | 7.8% | intergenic (+131/+14) | rraB → / ← yjgM | ribonuclease E inhibitor protein B/putative acetyltransferase YjgM |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196271 | 1211449 | 15179 | 13 [12] | [12] 13 | [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 | 3621200–3622305 | 3653116–3652031 | 29727–31917 | 13 [12] | [12] 13 | [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 | = 228108 | NA (NA) | 4 (0.090) | 4/256 | NT | NA | noncoding (2350/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | = 228124 | NA (NA) | noncoding (2366/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 1231303 | 43 (0.950) | 3 (0.070) | 3/250 | NT | 7.1% | coding (118/1269 nt) | umuC | DNA polymerase V catalytic protein |
| ? | NC_000913 | = 1231337 | 38 (0.880) | coding (152/1269 nt) | umuC | DNA polymerase V catalytic protein | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 40 (0.910) | 37/256 | 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 | 2729630 = | NA (NA) | 9 (0.210) | 6/254 | NT | NA | noncoding (1528/1542 nt) | rrsG | 16S ribosomal RNA |
| ? | NC_000913 | 2729652 = | NA (NA) | noncoding (1506/1542 nt) | rrsG | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 4066692 = | 74 (1.630) | 4 (0.090) | 3/256 | NT | 5.2% | coding (503/1386 nt) | yihP | putative 2,3‑dihydroxypropane‑1‑sulfonate export protein |
| ? | NC_000913 | 4066745 = | 75 (1.700) | coding (450/1386 nt) | yihP | putative 2,3‑dihydroxypropane‑1‑sulfonate export protein | |||||