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 | 104,031 | G→T | intergenic (+70/‑161) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 468,093 | Δ1 bp | coding (40/339 nt) | glnK → | nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB |
| RA | 1,191,676 | C→T | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,688 | C→T | T370T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,701 | T→C | L375M (TTA→CTG) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,703 | A→G | L375M (TTA→CTG) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,733 | C→T | N385N (AAC→AAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 2,054,744 | G→C | T224R (ACG→AGG) | nac ← | nitrogen assimilation regulon transcriptional regulator; autorepressor |
| RA | 2,718,735 | G→T | P124Q (CCG→CAG) | 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 | 3,304,872 | G→T | R58S (CGC→AGC) | rpsO ← | 30S ribosomal subunit protein S15 |
| RA | 4,175,524 | G→T | V83F (GTC→TTC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,390,235 | T→C | 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 | 345704 | 346935 | 1232 | 18 [17] | [16] 18 | prpC–[prpD] | prpC, [prpD] |
| * | * | ÷ | CP009273 | 748592 | 749952 | 1361 | 18 [16] | [17] 18 | gltA | gltA |
| * | * | ÷ | CP009273 | 1191736 | 1206911 | 15176 | 18 [17] | [17] 18 | [icd]–[icdC] | 25 genes [icd], ymfD, ymfE, lit, intE, xisE, ymfI, ymfJ, cohE, croE, ymfL, ymfM, oweE, aaaE, ymfR, beeE, jayE, ymfQ, stfP, tfaP, tfaE, stfE, pinE, mcrA, [icdC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | NA (NA) | 104 (2.240) | 73/290 | 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 | = 1391495 | NA (NA) | 48 (1.030) | 36/290 | 0.3 | 96.0% | 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) | 71 (1.540) | 44/288 | 0.1 | 97.3% | 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 = | 1 (0.020) | 55 (1.190) | 45/290 | 0.1 | 98.2% | 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 | 3 (0.060) | 47 (1.010) | 40/290 | 0.2 | 94.0% | 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 | |||||