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 | 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 | 600,233 | G→A | 12.7% | G507D (GGC→GAC) | cusA → | copper/silver export system RND permease |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 710,173 | A→G | 7.7% | intergenic (+57/+27) | chiQ → / ← fur | lipoprotein ChiQ/DNA‑binding transcriptional dual regulator Fur |
| RA | 710,436 | G→A | 100% | H71Y (CAC→TAC) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 759,250 | G→T | 100% | R182L (CGC→CTC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate 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 |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| 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 | 2,032,336 | G→C | 12.7% | intergenic (‑19/+48) | dcm ← / ← yedJ | DNA‑cytosine methyltransferase/putative HD superfamily phosphohydrolase YedJ |
| 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 | 2,225,493 | C→T | 7.5% | G47S (GGC→AGC) | yohC ← | putative inner membrane protein |
| JC JC | 2,391,775 | IS1 (+) +9 bp | 100% | coding (1259‑1267/1530 nt) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,483,912 | T→A | 11.0% | V53D (GTC→GAC) | evgA → | DNA‑binding transcriptional activator EvgA |
| RA | 2,561,205 | A→T | 10.5% | intergenic (+307/‑163) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein YffL/CPZ‑55 prophage; uncharacterized protein YffM |
| RA | 2,561,206 | A→T | 8.8% | intergenic (+308/‑162) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein YffL/CPZ‑55 prophage; uncharacterized protein YffM |
| RA | 2,637,438 | T→G | 12.5% | intergenic (‑82/+36) | der ← / ← bamB | 50S ribosomal subunit stability factor/outer membrane protein assembly factor BamB |
| RA | 2,661,969 | C→G | 100% | V55L (GTT→CTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 3,041,632 | T→A | 100% | V107E (GTG→GAG) | ygfZ → | folate‑binding protein |
| RA | 3,407,293 | T→A | 6.6% | intergenic (+27/‑82) | accC → / → yhdT | biotin carboxylase/DUF997 domain‑containing protein YhdT |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,578,609 | T→G | 8.3% | I40L (ATT→CTT) | gntR ← | DNA‑binding transcriptional repressor GntR |
| RA | 3,578,610 | C→A | 8.5% | K39N (AAG→AAT) | gntR ← | DNA‑binding transcriptional repressor GntR |
| 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] | |
| RA | 3,891,011 | C→T | 7.6% | A259V (GCG→GTG) | tnaB → | tryptophan:H(+) symporter TnaB |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,072,858 | G→A | 42.5% | A238A (GCC→GCT) | yihU ← | 3‑sulfolactaldehyde reductase |
| RA | 4,100,717 | G→T | 76.5% | intergenic (‑192/‑93) | rhaT ← / → sodA | rhamnose/lyxose:H(+) symporter/superoxide dismutase (Mn) |
| RA | 4,147,304 | G→C | 8.4% | R56P (CGG→CCG) | frwD → | putative PTS enzyme IIB component FrwD |
| RA | 4,158,785 | C→T | 100% | P99L (CCC→CTC) | oxyR → | DNA‑binding transcriptional dual regulator OxyR |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,196,196 | T→C | 100% | intergenic (‑97/+136) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,296,060 | C→T | 34.0% | 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 | 4,341,824 | T→G | 100% | intergenic (‑196/‑87) | melR ← / → melA | DNA‑binding transcriptional dual regulator MelR/alpha‑galactosidase |
| RA | 4,532,537 | G→C | 12.5% | A216G (GCC→GGC) | yjhP ← | KpLE2 phage‑like element; putative methyltransferase YjhP |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423765–3424234 | 3424522–3424239 | 6–758 | 13 [12] | [12] 13 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 315563 = | NA (NA) | 3 (0.070) | 3/244 | NT | NA | noncoding (335/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315599 = | NA (NA) | noncoding (371/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315646 | NA (NA) | 10 (0.230) | 10/254 | NT | NA | noncoding (418/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315665 | NA (NA) | noncoding (437/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315892 = | NA (NA) | 4 (0.090) | 3/258 | NT | NA | noncoding (664/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315923 = | NA (NA) | noncoding (695/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 392313 = | NA (NA) | 32 (0.740) | 14/256 | NT | NA | noncoding (654/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 392344 = | NA (NA) | noncoding (623/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 2298 (52.120) | 256/262 | NT | 98.3% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 40 (0.900) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 572471 | 40 (0.900) | 10 (0.300) +34 bp |
7/196 | NT | 27.3% | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein |
| ? | NC_000913 | 1095438 = | 32 (0.720) | noncoding (65/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 7 (0.160) | 13 (0.330) | 13/232 | NT | 68.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 6 (0.150) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 8 (0.180) | 11 (0.280) | 10/232 | NT | 62.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 6 (0.150) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1436548 = | 37 (0.830) | 21 (0.510) | 19/246 | NT | 37.0% | coding (346/1134 nt) | ompN | outer membrane porin N |
| ? | NC_000913 | = 1502024 | 37 (0.890) | coding (463/594 nt) | tehB | tellurite methyltransferase | |||||
| * | ? | NC_000913 | = 1463445 | 78 (1.760) | 5 (0.120) | 4/250 | NT | 6.1% | intergenic (+7/‑94) | paaK/paaX | phenylacetate‑CoA ligase/DNA‑binding transcriptional repressor PaaX |
| ? | NC_000913 | = 1463482 | 79 (1.880) | intergenic (+44/‑57) | paaK/paaX | phenylacetate‑CoA ligase/DNA‑binding transcriptional repressor PaaX | |||||
| * | ? | NC_000913 | = 2327312 | 42 (0.950) | 4 (0.100) | 4/238 | NT | 9.2% | intergenic (+19/+55) | atoB/yfaP | acetyl‑CoA acetyltransferase/DUF2135 domain‑containing protein YfaP |
| ? | NC_000913 | = 2327320 | 41 (1.020) | intergenic (+27/+47) | atoB/yfaP | acetyl‑CoA acetyltransferase/DUF2135 domain‑containing protein YfaP | |||||
| * | ? | NC_000913 | 2726200 = | NA (NA) | 3 (0.070) | 3/252 | NT | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA/23S ribosomal RNA |
| ? | NC_000913 | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | NC_000913 | 3521815 = | 33 (0.740) | 3 (0.070) | 3/246 | NT | 9.9% | coding (158/540 nt) | hofN | DNA utilization protein HofN |
| ? | NC_000913 | 3521857 = | 24 (0.580) | coding (116/540 nt) | hofN | DNA utilization protein HofN | |||||
| * | ? | NC_000913 | = 3741088 | NA (NA) | 4 (0.100) | 3/244 | NT | NA | intergenic (+130/+21) | avtA/ysaA | valine‑‑pyruvate aminotransferase/putative electron transport protein YsaA |
| ? | NC_000913 | = 3741092 | NA (NA) | intergenic (+134/+17) | avtA/ysaA | valine‑‑pyruvate aminotransferase/putative electron transport protein YsaA | |||||
| * | ? | NC_000913 | 4168332 = | 31 (0.700) | 6 (0.140) | 4/260 | NT | 16.4% | intergenic (+132/‑40) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| ? | NC_000913 | 4209776 = | NA (NA) | noncoding (3/76 nt) | gltV | tRNA‑Glu | |||||
| * | ? | NC_000913 | 4542682 = | 59 (1.330) | 4 (0.100) | 4/246 | NT | 7.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 41 (0.990) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||