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 | freq | annotation | gene | description |
| RA | 352,394 | A→G | 22.4% | E171E (GAA→GAG) | codA → | cytosine/isoguanine deaminase |
| RA | 982,565 | T→A | 100% | intergenic (‑127/+476) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 2,054,744 | G→C | 49.8% | T224R (ACG→AGG) | nac ← | nitrogen assimilation regulon transcriptional regulator; autorepressor |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 58.3% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,420,353 | A→G | 100% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,420,394 | G→T | 59.7% | intergenic (‑127/+94) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,529,057 | G→C | 39.0% | A545P (GCG→CCG) | ptsI → | PEP‑protein phosphotransferase of PTS system (enzyme I) |
| RA | 2,718,735 | G→T | 54.2% | P124Q (CCG→CAG) | kgtP ← | alpha‑ketoglutarate transporter |
| RA | 2,719,426 | T→C | 42.3% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,796,564 | G→A | 19.1% | V620I (GTT→ATT) | nrdE → | ribonucleoside‑diphosphate reductase 2, alpha subunit |
| JC JC | 3,178,254 | IS5 (+) +4 bp | 45.2% | coding (56‑59/291 nt) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,350,594 | G→A | 19.1% | T837T (ACG→ACA) | gltB → | glutamate synthase, large subunit |
| RA | 3,708,519 | G→A | 19.1% | N412N (AAC→AAT) | bisC ← | biotin sulfoxide reductase |
| RA | 4,175,524 | G→T | 61.5% | V83F (GTC→TTC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,390,235 | T→C | 50.7% | I44T (ATC→ACC) | 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 | 3365393 | 3365593 | 201 | 3 [2] | [2] 3 | nanT | sialic acid transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | NA (NA) | 31 (2.030) | 26/272 | NT | 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 = | 2 (0.130) | 17 (1.260) | 14/240 | NT | 81.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 6 (0.450) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 2 (0.130) | 11 (0.820) | 10/240 | NT | 73.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 6 (0.450) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1391495 | NA (NA) | 4 (0.260) | 4/272 | NT | 40.0% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | CP009273 | = 1972751 | 6 (0.390) | intergenic (‑297/‑483) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | = 1391495 | NA (NA) | 3 (0.200) | 3/272 | NT | 25.0% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | CP009273 | = 2083419 | 9 (0.590) | intergenic (‑225/‑58) | yefM/hisL | antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide | |||||
| * | ? | CP009273 | 2083598 = | 14 (0.920) | 5 (0.330) | 5/272 | NT | 27.0% | intergenic (+71/‑75) | hisL/hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| ? | CP009273 | 3713993 = | 13 (0.850) | intergenic (‑1/‑47) | mokA/insJ | pseudogene, overlapping regulatory peptide, enables hokB; completely contained in another CDS/IS150 transposase A | |||||
| * | ? | CP009273 | 2269338 = | 10 (0.660) | 3 (0.200) | 3/272 | NT | 23.1% | 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 | = 3360109 | NA (NA) | 9 (0.590) | 9/272 | NT | 56.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 3370794 = | 7 (0.460) | intergenic (‑15/+380) | sspA/rpsI | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9 | |||||