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 | freq | annotation | gene | description |
| RA | 119,114 | Δ1 bp | 12.1% | coding (382/552 nt) | ampD → | 1,6‑anhydro‑N‑acetylmuramoyl‑L‑alanine amidase |
| RA | 119,115 | Δ1 bp | 12.1% | coding (383/552 nt) | ampD → | 1,6‑anhydro‑N‑acetylmuramoyl‑L‑alanine amidase |
| 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 | 397,574 | C→T | 18.9% | L312L (CTC→CTT) | sbmA → | peptide antibiotic/peptide nucleic acid transporter |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| 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 | 2,132,787 | 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 |
| JC JC | 2,391,775 | IS1 (+) +9 bp | 100% | coding (1259‑1267/1530 nt) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,425,968 | T→G | 12.1% | intergenic (‑52/+38) | hisQ ← / ← hisJ | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisQ/histidine ABC transporter periplasmic binding protein |
| RA | 2,661,969 | C→G | 100% | V55L (GTT→CTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,740,698 | C→T | 10.3% | P151P (CCG→CCA) | aroF ← | 3‑deoxy‑7‑phosphoheptulonate synthase, Tyr‑sensitive |
| RA | 3,041,632 | T→A | 100% | V107E (GTG→GAG) | ygfZ → | folate‑binding protein |
| RA | 3,080,006 | T→C | 11.8% | K544E (AAA→GAA) | tktA ← | transketolase 1 |
| RA | 3,168,653 | G→A | 8.5% | intergenic (‑109/+96) | mqsR ← / ← ygiV | mRNA interferase/toxin of the MqsR‑MqsA toxin‑antitoxin system/DNA‑binding transcriptional repressor YgiV |
| RA | 3,288,032 | C→A | 8.5% | intergenic (+22/‑58) | yraH → / → yraI | putative fimbrial protein YraH/putative fimbrial chaperone YraI |
| RA | 3,288,033 | T→G | 8.6% | intergenic (+23/‑57) | yraH → / → yraI | putative fimbrial protein YraH/putative fimbrial chaperone YraI |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| 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 | 3,971,996 | T→A | 12.7% | L246Q (CTG→CAG) | wecC → | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,094,415 | T→G | 11.8% | intergenic (‑143/+308) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,196,196 | T→C | 32.6% | intergenic (‑97/+136) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,196,249 | C→A | 17.7% | intergenic (‑150/+83) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,273,362 | T→A | 24.4% | A170A (GCA→GCT) | uvrA ← | excision nuclease subunit A |
| RA | 4,296,060 | C→T | 38.5% | 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 | 33.8% | intergenic (‑196/‑87) | melR ← / → melA | DNA‑binding transcriptional dual regulator MelR/alpha‑galactosidase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 4168393–4168478 | 4171534–4168511 | 34–3142 | 9 [7] | [8] 10 | [gltT]–[rrlB] | [gltT],[rrlB] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 304784 = | 34 (1.000) | 3 (0.090) | 3/252 | NT | 8.6% | coding (422/711 nt) | ecpE | putative fimbrial chaperone EcpE |
| ? | NC_000913 | 304813 = | 31 (0.950) | coding (393/711 nt) | ecpE | putative fimbrial chaperone EcpE | |||||
| * | ? | NC_000913 | 315563 = | NA (NA) | 3 (0.100) | 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 | = 315852 | NA (NA) | 19 (0.580) | 8/256 | NT | NA | noncoding (624/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315875 | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315916 | NA (NA) | 7 (0.210) | 5/256 | NT | NA | noncoding (688/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315925 | NA (NA) | noncoding (697/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 392648 = | NA (NA) | 4 (0.120) | 3/250 | NT | NA | noncoding (319/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 392679 = | NA (NA) | noncoding (288/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 1534 (45.410) | 248/262 | NT | 98.9% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 17 (0.500) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | 1207790 = | 3 (0.090) | 16 (0.540) | 15/232 | NT | 80.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 5 (0.170) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 3 (0.090) | 13 (0.430) | 12/232 | NT | 77.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 5 (0.170) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 2729475 = | 24 (0.700) | 3 (0.100) | 3/244 | NT | 14.9% | intergenic (‑31/+141) | gltW/rrsG | tRNA‑Glu/16S ribosomal RNA |
| ? | NC_000913 | = 4168363 | 12 (0.380) | intergenic (+163/‑9) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu | |||||
| * | ? | NC_000913 | 2729955 = | NA (NA) | 3 (0.090) | 3/252 | NT | NA | noncoding (1203/1542 nt) | rrsG | 16S ribosomal RNA |
| ? | NC_000913 | 2729972 = | NA (NA) | noncoding (1186/1542 nt) | rrsG | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 3847998 | 26 (0.760) | 3 (0.090) | 3/256 | NT | 10.5% | coding (627/1320 nt) | uhpC | inner membrane protein sensing glucose‑6‑phosphate |
| ? | NC_000913 | = 3848018 | 26 (0.790) | coding (607/1320 nt) | uhpC | inner membrane protein sensing glucose‑6‑phosphate | |||||
| * | ? | NC_000913 | 4542682 = | 37 (1.090) | 4 (0.130) | 4/246 | NT | 11.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 26 (0.820) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||