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 | 66,528 | T→C | Q8R (CAG→CGG) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase AraD |
| MC JC | 66,533 | 3540 bp→27 bp | [araD]–araB | [araD], araA, araB | |
| RA | 70,289 | G→T | intergenic (‑241/‑98) | araB ← / → araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 366,519 | G→A | A331V (GCG→GTG) | lacI ← | DNA‑binding transcriptional repressor LacI |
| JC JC | 371,758 | IS30 (+) +2 bp | coding (520‑521/867 nt) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase |
| RA | 503,429 | C→T | intergenic (‑191/+47) | ybaL ← / ← fsr | putative transporter YbaL/fosmidomycin efflux pump |
| RA | 705,013 | T→C | L357S (TTG→TCG) | nagE → | N‑acetylglucosamine‑specific PTS enzyme IIABC component |
| RA | 1,291,496 | C→T | P14S (CCC→TCC) | galU → | UTP‑‑glucose‑1‑phosphate uridylyltransferase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,970 | +GT | coding (789/1632 nt) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,310,770 | A→G | H32H (CAT→CAC) | yciI ← | protein YciI |
| RA | 1,310,841 | C→T | D9N (GAC→AAC) | yciI ← | protein YciI |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,655,795 | IS2 (–) +5 bp | intergenic (‑122/‑9) | ynfA ← / → ynfB | putative transporter YnfA/DUF1283 domain‑containing protein YnfB |
| RA | 1,695,565 | C→T | G169G (GGG→GGA) | uidA ← | beta‑glucuronidase |
| RA | 1,699,275 | C→T | intergenic (‑95/‑80) | malI ← / → malX | DNA‑binding transcriptional repressor MalI/PTS enzyme IIBC component MalX |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,823,288 | C→T | G161D (GGC→GAC) | recA ← | DNA recombination/repair protein RecA |
| RA | 3,070,858 | T→G | K129N (AAA→AAC) | fbaA ← | fructose‑bisphosphate aldolase class II |
| RA | 3,110,421 | C→A | noncoding (56/76 nt) | pheV → | tRNA‑Phe |
| RA | 3,329,771 | G→A | W270* (TGG→TAG) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,792,007 | C→G | G182A (GGT→GCT) | kbl ← | 2‑amino‑3‑ketobutyrate CoA ligase |
| RA | 4,093,770 | C→T | G168D (GGC→GAC) | rhaD ← | rhamnulose‑1‑phosphate aldolase |
| RA | 4,161,248 | G→T | G61V (GGC→GTC) | fabR → | DNA‑binding transcriptional repressor FabR |
| RA | 4,164,123 | C→G | A162G (GCA→GGA) | btuB → | cobalamin outer membrane transporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,474,834 | A→G | intergenic (+117/‑28) | bdcR → / → tabA | putative transcriptional regulator BdcR/DUF386 domain‑containing toxin‑antitoxin biofilm protein TabA |
| RA | 4,585,480 | G→A | Q428* (CAA→TAA) | hsdR ← | type I restriction enzyme EcoKI endonuclease subunit |
| RA | 4,602,509 | C→T | W117* (TGG→TAG) | yjjP ← | putative succinate exporter YjjP |
| RA | 4,616,669 | G→T | L133I (CTA→ATA) | yjjI ← | DUF3029 domain‑containing protein YjjI |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 364356 | 366418 | 2063 | 14 [0] | [0] 4 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_000913 | 417193 | 419181 | 1989 | 2 [0] | [0] 26 | [phoB]–[phoR] | [phoB],[phoR] |
| * | * | ÷ | NC_000913 | 987452 | 987540 | 89 | 2 [1] | [1] 3 | ompF/asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| * | * | ÷ | NC_000913 | 1544910 | 1544995 | 86 | 2 [1] | [0] 2 | yddK | leucine‑rich repeat domain‑containing protein YddK |
| * | * | ÷ | NC_000913 | 1638685 | 1638844 | 160 | 2 [1] | [1] 2 | cspI/rzpQ | cold shock‑like protein CspI/DUF2514 domain‑containing protein RzpQ |
| * | * | ÷ | NC_000913 | 1694867 | 1695469 | 603 | 2 [1] | [1] 7 | uidA | beta‑glucuronidase |
| * | * | ÷ | NC_000913 | 2343845 | 2343865 | 21 | 3 [1] | [1] 2 | yfaL | putative autotransporter adhesin YfaL |
| * | * | ÷ | NC_000913 | 2521007 | 2521087 | 81 | 10 [0] | [1] 3 | [valX] | [valX] |
| * | * | ÷ | NC_000913 | 2784234 | 2784305 | 72 | 2 [0] | [0] 2 | ypjB | DUF5508 domain‑containing protein YpjB |
| * | * | ÷ | NC_000913 | 3090238 | 3090723 | 486 | 53 [0] | [1] 2 | [yggI]–[endA] | [yggI],[endA] |
| * | * | ÷ | NC_000913 | 3423907–3424233 | 3424405–3424238 | 6–499 | 2 [1] | [1] 2 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4093991 | 4095331 | 1341 | 63 [1] | [1] 2 | [rhaD]–[rhaA] | [rhaD],[rhaA] |
| * | * | ÷ | NC_000913 | 4095478 | 4095793 | 316 | 2 [1] | [1] 2 | rhaA | L‑rhamnose isomerase |
| * | * | ÷ | NC_000913 | 4096099 | 4097258 | 1160 | 2 [0] | [1] 2 | rhaB | rhamnulokinase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 364355 | 0 (0.000) | 9 (0.310) +41 bp |
8/400 | 1.3 | 73.1% | coding (1951/3075 nt) | lacZ | beta‑galactosidase |
| ? | NC_000913 | = 4171921 | 8 (0.230) | intergenic (+165/‑136) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | = 417138 | 2 (0.060) | 23 (0.780) +37 bp |
23/408 | 0.3 | 96.5% | intergenic (‑186/‑4) | sbcD/phoB | ATP‑dependent structure‑specific DNA nuclease ‑ SbcD subunit/DNA‑binding transcriptional dual regulator PhoB |
| ? | NC_000913 | 419182 = | 0 (0.000) | coding (1294/1296 nt) | phoR | sensor histidine kinase PhoR | |||||
| * | ? | NC_000913 | 1207790 = | 15 (0.430) | 7 (0.220) | 7/450 | 1.6 | 41.2% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 6 (0.190) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.430) | 8 (0.250) | 8/450 | 1.4 | 44.4% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 6 (0.190) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 2521006 | 0 (0.000) | 10 (0.420) | 9/330 | 0.9 | 100% | noncoding (76/76 nt) | valU | tRNA‑Val |
| ? | NC_000913 | 2521127 = | 0 (0.000) | intergenic (+1/‑46) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | = 3090237 | 0 (0.000) | 35 (1.460) +74 bp |
33/334 | 0.1 | 98.1% | coding (483/498 nt) | yggI | protein YggI |
| ? | NC_000913 | 3090926 = | 2 (0.060) | coding (580/708 nt) | endA | DNA‑specific endonuclease I | |||||
| * | ? | NC_000913 | = 4093990 | 1 (0.030) | 54 (1.770) +29 bp |
46/424 | 0.0 | 97.6% | coding (283/825 nt) | rhaD | rhamnulose‑1‑phosphate aldolase |
| ? | NC_000913 | 4097452 = | 2 (0.060) | intergenic (‑4/‑284) | rhaB/rhaS | rhamnulokinase/DNA‑binding transcriptional activator RhaS | |||||
| * | ? | NC_000913 | 4171749 = | 16 (0.460) | 8 (0.240) +GGAATTAATT |
7/462 | 1.6 | 41.0% | noncoding (113/120 nt) | rrfB | 5S ribosomal RNA |
| ? | NC_000913 | = 4171921 | 8 (0.230) | intergenic (+165/‑136) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||