mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 753,013 | G→T | E551* (GAA→TAA) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 2,718,678 | C→G | G143A (GGC→GCC) | kgtP ← | alpha‑ketoglutarate transporter |
| RA | 2,719,426 | T→C | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,861,917 | G→A | Q66* (CAG→TAG) | nlpD ← | activator of AmiC murein hydrolase activity, lipoprotein |
| RA | 2,870,339 | G→A | G134S (GGC→AGC) | iap → | aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 3,019,631 | G→T | M169I (ATG→ATT) | guaD → | guanine deaminase |
| RA | 3,029,079 | C→T | A188T (GCT→ACT) | prfB ← | peptide chain release factor RF‑2 |
| RA | 3,204,161 | G→A | E8K (GAA→AAA) | rpsU → | 30S ribosomal subunit protein S21 |
| RA | 4,176,029 | C→A | P251Q (CCG→CAG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,183,494 | C→A | R4L (CGT→CTT) | thiF ← | adenylyltransferase, modifies ThiS C‑terminus |
| RA | 4,390,205 | G→T | G34V (GGG→GTG) | hfq → | global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 345704 | 346929 | 1226 | 23 [21] | [21] 22 | prpC–[prpD] | prpC, [prpD] |
| * | * | ÷ | CP009273 | 748611 | 749983 | 1373 | 22 [21] | [21] 22 | gltA | gltA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | NA (NA) | 106 (1.970) | 69/290 | 0.0 | NA | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 1203246 = | 9 (0.170) | 43 (0.900) | 38/258 | 0.3 | 86.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 6 (0.130) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 9 (0.170) | 49 (1.020) | 39/258 | 0.2 | 87.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 6 (0.130) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1391495 | NA (NA) | 47 (0.870) | 42/290 | 0.3 | 95.9% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | CP009273 | = 1972751 | 2 (0.040) | intergenic (‑297/‑483) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 1972748 = | 2 (0.040) | 63 (1.180) | 38/288 | 0.5 | 96.9% | intergenic (‑294/‑486) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 2283592 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | 2269338 = | 3 (0.060) | 44 (0.820) | 39/290 | 0.4 | 93.6% | coding (587/1026 nt) | yejE | microcin C transporter YejABEF, permease subunit; ABC family |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2269346 | 6 (0.110) | 53 (0.980) | 44/290 | 0.2 | 89.8% | coding (595/1026 nt) | yejE | microcin C transporter YejABEF, permease subunit; ABC family |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||