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 |
| RA | 70,289 | G→T | intergenic (‑241/‑98) | araB ← / → araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| RA | 70,371 | T→C | intergenic (‑323/‑16) | araB ← / → araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| RA | 70,434 | C→T | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 70,581 | C→T | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 70,740 | T→G | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 71,109 | T→C | T241T (ACT→ACC) | araC → | DNA‑binding transcriptional dual regulator AraC |
| MC JC | 147,727 | Δ12 bp | coding (760‑771/903 nt) | rpnC → | recombination‑promoting nuclease RpnC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 566,173 | C→G | pseudogene (189/264 nt) | exoD ← | DLP12 prophage; putative exonuclease ExoD |
| RA | 566,205 | T→C | pseudogene (157/264 nt) | exoD ← | DLP12 prophage; putative exonuclease ExoD |
| RA | 566,245 | G→A | pseudogene (117/264 nt) | exoD ← | DLP12 prophage; putative exonuclease ExoD |
| RA | 566,277 | C→T | pseudogene (85/264 nt) | exoD ← | DLP12 prophage; putative exonuclease ExoD |
| RA | 566,323 | C→T | pseudogene (39/264 nt) | exoD ← | DLP12 prophage; putative exonuclease ExoD |
| RA | 1,143,998 | C→T | G124S (GGT→AGT) | rne ← | ribonuclease E |
| JC JC | 1,293,033 | IS1 (+) +9 bp | intergenic (‑111/‑486) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,917,345 | G→A | G763G (GGG→GGA) | barA → | sensory histidine kinase BarA |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,566,544 | C→A | S13I (AGC→ATC) | glgP ← | glycogen phosphorylase |
| MC JC | 3,815,859 | Δ82 bp | [rph] | [rph] | |
| RA | 4,128,259 | A→G | V46A (GTG→GCG) | metJ ← | DNA‑binding transcriptional repressor MetJ |
| RA | 4,128,264 | A→T | R44R (CGT→AGA) | metJ ← | DNA‑binding transcriptional repressor MetJ |
| RA | 4,128,266 | G→T | R44R (CGT→AGA) | metJ ← | DNA‑binding transcriptional repressor MetJ |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423810–3424234 | 3424503–3424238 | 5–694 | 4 [0] | [0] 2 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 15681 = | NA (NA) | 3 (0.020) | 3/286 | 2.3 | NA | noncoding (295/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 15723 = | NA (NA) | noncoding (337/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 20044 | NA (NA) | 6 (0.030) | 4/286 | 2.2 | NA | noncoding (520/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 20084 | NA (NA) | noncoding (480/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 224374 | NA (NA) | 7 (0.040) | 5/282 | 2.0 | NA | noncoding (604/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | = 224403 | NA (NA) | noncoding (633/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 224575 = | NA (NA) | 6 (0.030) | 3/282 | 2.3 | NA | noncoding (805/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | 224623 = | NA (NA) | noncoding (853/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 224581 | NA (NA) | 4 (0.020) | 3/282 | 2.3 | NA | noncoding (811/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | = 224615 | NA (NA) | noncoding (845/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 224598 | NA (NA) | 3 (0.020) | 3/280 | 2.3 | NA | noncoding (828/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | = 224641 | NA (NA) | noncoding (871/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 258341 | NA (NA) | 3 (0.020) | 3/284 | 2.3 | NA | noncoding (335/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 279558 | NA (NA) | noncoding (373/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 274347 = | NA (NA) | 11 (0.060) | 6/282 | 1.9 | NA | noncoding (803/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274410 = | NA (NA) | noncoding (740/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 26 (0.140) | 7/278 | 1.8 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 274695 | NA (NA) | 15 (0.080) | 8/288 | 1.8 | NA | noncoding (455/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 274727 | NA (NA) | noncoding (423/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 316201 | NA (NA) | 17 (0.090) | 7/278 | 1.8 | NA | noncoding (973/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316220 | NA (NA) | noncoding (992/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 349797 | NA (NA) | 3 (0.020) | 3/282 | 2.3 | NA | noncoding (6/36 nt) | other | REP25e |
| ? | NC_000913 | = 349908 | NA (NA) | noncoding (24/36 nt) | other | REP25g | |||||
| * | ? | NC_000913 | 381663 = | NA (NA) | 8 (0.040) | 4/282 | 2.1 | NA | noncoding (404/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381703 = | NA (NA) | noncoding (444/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 381669 | NA (NA) | 12 (0.070) | 8/282 | 1.8 | NA | noncoding (410/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381695 | NA (NA) | noncoding (436/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 381681 = | NA (NA) | 6 (0.030) | 5/278 | 2.0 | NA | noncoding (422/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381753 = | NA (NA) | noncoding (494/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 382323 | NA (NA) | 3 (0.020) | 3/286 | 2.3 | NA | noncoding (1064/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382348 | NA (NA) | noncoding (1089/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 526459 = | NA (NA) | 7 (0.040) | 5/286 | 2.0 | 100% | coding (3199/4281 nt) | rhsD | protein RhsD |
| ? | NC_000913 | 526482 = | 0 (0.000) | coding (3222/4281 nt) | rhsD | protein RhsD | |||||
| * | ? | NC_000913 | = 1180368 | NA (NA) | 3 (0.020) | 3/284 | 2.3 | NA | noncoding (14/29 nt) | other | REPv104a |
| ? | NC_000913 | = 1180429 | NA (NA) | noncoding (22/34 nt) | other | REP104b | |||||
| * | ? | NC_000913 | 1207790 = | 41 (0.210) | 28 (0.160) | 21/264 | 1.1 | 44.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 33 (0.190) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 41 (0.210) | 51 (0.300) | 39/264 | 0.7 | 59.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 33 (0.190) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 128 (0.690) | 84/288 | 0.3 | 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 | 1396531 = | NA (NA) | 62 (0.340) | 10/284 | 1.6 | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2304533 | NA (NA) | 8 (0.040) | 5/290 | 2.0 | NA | noncoding (32/34 nt) | other | REP161c |
| ? | NC_000913 | = 2304902 | NA (NA) | noncoding (2/34 nt) | other | REP161i | |||||
| * | ? | NC_000913 | = 2304789 | NA (NA) | 6 (0.040) +33 bp |
3/230 | 2.2 | NA | noncoding (2/34 nt) | other | REP161g |
| ? | NC_000913 | = 2305065 | NA (NA) | noncoding (29/36 nt) | other | REP161l | |||||
| * | ? | NC_000913 | = 2730286 | NA (NA) | 7 (0.040) | 4/280 | 2.1 | NA | noncoding (872/1542 nt) | rrsG | 16S ribosomal RNA |
| ? | NC_000913 | = 2730329 | NA (NA) | noncoding (829/1542 nt) | rrsG | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 2822705 = | 139 (0.720) | 518 (3.310) +27 bp |
103/242 | 0.1 | 73.8% | intergenic (‑66/+3) | recX/recA | RecA inhibitor RecX/DNA recombination/repair protein RecA |
| ? | NC_000913 | 4171753 = | 311 (1.620) | noncoding (117/120 nt) | rrfB | 5S ribosomal RNA | |||||
| * | ? | NC_000913 | 3620119 = | NA (NA) | 3 (0.020) | 3/284 | 2.3 | 100% | coding (928/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3620146 = | 0 (0.000) | coding (955/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 3620123 = | NA (NA) | 3 (0.020) | 3/284 | 2.3 | 100% | coding (932/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3620147 = | 0 (0.000) | coding (956/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 3620220 | NA (NA) | 8 (0.040) | 7/284 | 1.8 | 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 | = 3620350 | NA (NA) | 7 (0.040) | 4/284 | 2.2 | 100% | coding (1159/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3620425 | 0 (0.000) | coding (1234/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 3620351 = | NA (NA) | 5 (0.030) | 3/290 | 2.3 | 100% | coding (1160/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3620387 = | 0 (0.000) | coding (1196/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 3621583 | NA (NA) | 12 (0.070) | 8/284 | 1.8 | 100% | coding (2392/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3621667 | 0 (0.000) | coding (2476/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 3625635 = | NA (NA) | 10 (0.050) | 7/284 | 1.8 | NA | intergenic (+121/+44) | yhhI/yhhJ | putative transposase/ABC transporter family protein YhhJ |
| ? | NC_000913 | 3625669 = | NA (NA) | noncoding (3/28 nt) | other | REPv260b | |||||