mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 173,350 | T→C | M630T (ATG→ACG) | fhuB → | iron(III) hydroxamate ABC transporter membrane subunit |
| JC JC | 253,485 | IS3 (–) +3 bp | intergenic (+324/+772) | yafP → / ← pepD | putative N‑acetyltransferase YafP/peptidase D |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 572,138 | IS2 (+) +5 bp | coding (685‑689/798 nt) | ybcM → | putative DNA‑binding transcriptional regulator |
| JC JC | 820,823 | IS5 (–) +4 bp | coding (31‑34/714 nt) | ybhM → | Bax1‑I family protein YbhM |
| RA | 882,616 | C→T | R40H (CGC→CAC) | deoR ← | DNA‑binding transcriptional repressor DeoR |
| RA | 1,076,997 | C→T | R629H (CGC→CAC) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,093,264 | C→T | A130V (GCA→GTA) | dgcT → | putative diguanylate cyclase DgcT |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,306,423 | (T)5→4 | coding (660/1005 nt) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| MC JC | 1,397,239 | Δ10,478 bp | IS5‑mediated | ynaJ–[dgcM] | ynaJ, uspE, fnr, ogt, abgT, abgB, abgA, abgR, mcaS, smrA, [dgcM] |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,844,295 | C→T | G193R (GGA→AGA) | ynjI ← | DUF1266 domain‑containing protein YnjI |
| JC JC | 1,859,380 | IS5 (+) +4 bp | coding (847‑850/1380 nt) | ydjK ← | putative transporter YdjK |
| JC JC | 1,909,378 | IS2 (–) +5 bp | coding (718‑722/792 nt) | kdgR ← | DNA‑binding transcriptional repressor KdgR |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| JC JC | 2,034,215 | IS3 (+) +3 bp | intergenic (+476/‑1618) | rseX → / → hchA | small regulatory RNA RseX/protein/nucleic acid deglycase 1 |
| RA | 2,043,522 | C→A | noncoding (36/90 nt) | serU ← | tRNA‑Ser |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,317,455 | IS2 (–) +5 bp | coding (2418‑2422/2850 nt) | rcsC ← | histidine kinase RcsC |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,730,875 | A→C | noncoding (283/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 2,755,949 | T→C | noncoding (357/363 nt) | ssrA → | tmRNA |
| RA | 2,774,947 | G→A | G544S (GGT→AGT) | yfjW → | uncharacterized protein YfjW |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,486,241 | A→C | Y41S (TAC→TCC) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,948,012 | G→T | intergenic (‑45/‑74) | hdfR ← / → maoP | DNA‑binding transcriptional dual regulator HdfR/macrodomain Ori protein |
| JC JC | 4,123,618 | IS1 (–) +8 bp | coding (832‑839/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| 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 | 173541 | 174915 | 1375 | 25 [24] | [24] 25 | hemL | hemL |
| * | * | ÷ | NC_000913 | 257886 | 258675–257909 | 24–790 | 100 [0] | [0] 87 | [crl]–insA9 | [crl],insB9,insA9 |
| * | * | ÷ | NC_000913 | 1196304 | 1211487 | 15184 | 26 [24] | [24] 25 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 104 [0] | [0] 114 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423895–3424234 | 3424459–3424238 | 5–565 | 25 [24] | [24] 25 | rrlD | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257885 | 0 (0.000) | 100 (1.210) | 73/598 | 0.1 | 100% | pseudogene (57/71 nt) | crl | RNA polymerase holoenzyme assembly factor Crl |
| ? | NC_000913 | 391709 = | NA (NA) | noncoding (1258/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 258676 = | 0 (0.000) | 84 (1.080) +CGAATATACGGGCCTAG |
61/564 | 0.1 | 100% | pseudogene (1/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl |
| ? | NC_000913 | = 392966 | NA (NA) | noncoding (1/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 567858 = | 3 (0.040) | 71 (0.860) | 51/596 | 0.4 | 96.0% | noncoding (1082/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 568034 | NA (NA) | noncoding (1258/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 103 (1.250) | 72/598 | 0.1 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 114 (1.380) | 72/598 | 0.1 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 75 (0.910) | 52/598 | 0.4 | NA | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | 3762460 = | NA (NA) | coding (278/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3722075 | NA (NA) | 93 (1.130) | 56/598 | 0.3 | 98.9% | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 3762462 | 1 (0.010) | coding (280/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 94 (1.140) | 46 (0.570) | 37/580 | 1.0 | 33.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 91 (1.140) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 104 (1.260) | 38 (0.470) | 31/580 | 1.5 | 28.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 91 (1.140) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||