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 | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| JC JC | 1,293,032 | IS1 (–) +8 bp | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,806,340 | C→T | intergenic (‑257/‑30) | ydiY ← / → pfkB | acid‑inducible putative outer membrane protein/6‑phosphofructokinase II |
| RA | 1,807,103 | C→A | P245Q (CCG→CAG) | pfkB → | 6‑phosphofructokinase II |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 3,560,455 | +G | 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 |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,645 | Δ5 bp | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1311639 | 1311665 | 27 | 5 [3] | [4] 6 | tonB | membrane spanning protein in TonB‑ExbB‑ExbD transport complex |
| * | * | ÷ | NC_000913 | 2066270–2066600 | 2066600 | 1–331 | 5 [4] | [3] 5 | [insH1] | [insH1] |
| * | * | ÷ | NC_000913 | 3423765–3424234 | 3424515–3424238 | 5–751 | 7 [4] | [2] 5 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4107560 | 4108491 | 932 | 5 [1] | [0] 6 | pfkA | 6‑phosphofructokinase I |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 225468 = | 2 (0.070) | 11 (0.400) | 11/204 | 1.3 | 85.7% | intergenic (+11/‑32) | ileV/alaV | tRNA‑Ile/tRNA‑Ala |
| ? | NC_000913 | = 3427068 | NA (NA) | intergenic (‑35/+8) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | NC_000913 | = 225895 | NA (NA) | 11 (0.390) | 9/208 | 1.7 | NA | noncoding (137/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 225899 | NA (NA) | noncoding (141/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 228108 | NA (NA) | 4 (0.140) | 4/214 | 3.0 | NA | noncoding (2350/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 228124 | NA (NA) | noncoding (2366/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 4 (0.140) | 4/204 | 2.9 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 382282 = | NA (NA) | 4 (0.140) | 4/210 | 3.0 | NA | noncoding (1023/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 382313 = | NA (NA) | noncoding (1054/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 519442 | 17 (0.570) | 6 (0.210) | 5/206 | 2.6 | 25.1% | coding (324/627 nt) | tesA | acyl‑CoA thioesterase 1 and protease I and lysophospholipase L1 |
| ? | NC_000913 | = 519458 | 20 (0.720) | coding (308/627 nt) | tesA | acyl‑CoA thioesterase 1 and protease I and lysophospholipase L1 | |||||
| * | ? | NC_000913 | = 823993 | 12 (0.400) | 6 (0.210) | 6/210 | 2.4 | 33.0% | coding (505/762 nt) | ybhP | endo/exonuclease/phosphatase family protein |
| ? | NC_000913 | = 824001 | 13 (0.460) | coding (497/762 nt) | ybhP | endo/exonuclease/phosphatase family protein | |||||
| * | ? | NC_000913 | = 859192 | 29 (0.960) | 7 (0.250) | 7/206 | 2.1 | 21.2% | intergenic (‑131/+21) | ybiU/ybiV | DUF1479 family protein/sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase |
| ? | NC_000913 | = 859197 | 25 (0.900) | intergenic (‑136/+16) | ybiU/ybiV | DUF1479 family protein/sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase | |||||
| * | ? | NC_000913 | 974765 = | 11 (0.370) | 4 (0.140) | 4/210 | 3.0 | 35.7% | coding (447/1323 nt) | mukF | chromosome condensin MukBEF, kleisin‑like subunit, binds calcium |
| ? | NC_000913 | 974803 = | 4 (0.140) | coding (485/1323 nt) | mukF | chromosome condensin MukBEF, kleisin‑like subunit, binds calcium | |||||
| * | ? | NC_000913 | 1207790 = | 3 (0.100) | 11 (0.430) | 11/190 | 1.2 | 79.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 3 (0.120) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 3 (0.100) | 18 (0.700) | 16/190 | 0.6 | 86.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 3 (0.120) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1269811 = | 22 (0.730) | 6 (0.210) | 5/206 | 2.6 | 23.3% | intergenic (‑1/‑47) | ldrB/rdlB | toxic polypeptide, small/sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB |
| ? | NC_000913 | 1270384 = | 19 (0.680) | intergenic (‑39/‑9) | ldrC/rdlC | toxic polypeptide, small/sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC | |||||
| * | ? | NC_000913 | 1633479 = | 0 (0.000) | 4 (0.140) | 4/208 | 2.9 | 72.7% | intergenic (+174/‑143) | ydfK/pinQ | cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase |
| ? | NC_000913 | 1633499 = | 3 (0.110) | intergenic (+194/‑123) | ydfK/pinQ | cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase | |||||
| * | ? | NC_000913 | 1876115 = | 25 (0.830) | 6 (0.220) | 5/204 | 2.6 | 24.0% | coding (443/1182 nt) | yeaN | putative MFS transporter, inner membrane protein |
| ? | NC_000913 | 1876150 = | 15 (0.540) | coding (478/1182 nt) | yeaN | putative MFS transporter, inner membrane protein | |||||
| * | ? | NC_000913 | 1941819 = | 30 (1.000) | 8 (0.290) | 8/206 | 1.9 | 23.2% | coding (765/933 nt) | znuA | zinc ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1941845 = | 25 (0.900) | coding (739/933 nt) | znuA | zinc ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 2146653 | NA (NA) | 4 (0.140) | 4/208 | 2.9 | NA | noncoding (54/84 nt) | REP147 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP147 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 2146683 | NA (NA) | noncoding (84/84 nt) | REP147 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP147 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | 2590715 = | 12 (0.400) | 5 (0.190) | 5/198 | 2.5 | 25.8% | intergenic (+7/+92) | acrD/ypfM | aminoglycoside/multidrug efflux system/stress‑induced small enterobacterial protein |
| ? | NC_000913 | 2590747 = | 18 (0.670) | intergenic (+39/+60) | acrD/ypfM | aminoglycoside/multidrug efflux system/stress‑induced small enterobacterial protein | |||||
| * | ? | NC_000913 | 3470277 = | NA (NA) | 6 (0.210) | 5/208 | 2.6 | NA | coding (1053/1185 nt) | tufA | translation elongation factor EF‑Tu 1 |
| ? | NC_000913 | 3470311 = | NA (NA) | coding (1019/1185 nt) | tufA | translation elongation factor EF‑Tu 1 | |||||
| * | ? | NC_000913 | 4213631 = | 19 (0.630) | 5 (0.180) | 5/210 | 2.6 | 20.4% | intergenic (+14/+49) | yjaA/yjaB | stress‑induced protein/GNAT‑family putative N‑acetyltransferase; acetyl coenzyme A‑binding protein |
| ? | NC_000913 | 4213662 = | 21 (0.740) | intergenic (+45/+18) | yjaA/yjaB | stress‑induced protein/GNAT‑family putative N‑acetyltransferase; acetyl coenzyme A‑binding protein | |||||