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 | 444,779 | C→T | 77.2% | W440* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 788,752 | C→A | 12.1% | G165C (GGC→TGC) | modF ← | fused molybdate transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 1,191,676 | C→T | 27.4% | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,688 | C→T | 21.2% | T370T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,701 | T→C | 23.8% | L375L (TTA→CTA) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,703 | A→G | 21.8% | L375L (TTA→TTG) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,207,564 | A→T | 13.8% | intergenic (‑105/+595) | iraM ← / ← ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| RA | 2,007,748 | C→T | 17.4% | P347S (CCG→TCG) | fliF → | flagellar basal‑body MS‑ring and collar protein |
| RA | 2,142,095 | G→A | 14.9% | R314H (CGC→CAC) | yegD → | Hsp70 chaperone family protein |
| JC JC | 2,215,619 | IS2 (+) +5 bp | 33.3% | intergenic (‑151/‑41) | bglX ← / → dld | beta‑D‑glucoside glucohydrolase, periplasmic/D‑lactate dehydrogenase, FAD‑binding, NADH independent |
| RA | 2,305,991 | G→T | 57.2% | Q80K (CAG→AAG) | ompC ← | outer membrane porin protein C |
| RA | 2,419,720 | T→C | 45.1% | D183G (GAT→GGT) | hisJ ← | histidine/lysine/arginine/ornithine transporter subunit |
| RA | 2,420,353 | A→G | 67.6% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,574,250 | G→A | 18.2% | G419D (GGC→GAC) | tktB → | transketolase 2, thiamine triphosphate‑binding |
| RA | 3,165,217 | A→T | 15.3% | intergenic (+25/+21) | qseC → / ← ygiZ | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein |
| RA | 3,371,135 | G→T | 25.0% | intergenic (‑356/+39) | 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 |
| JC | 3,528,829:1 | (GTTTTCAGCCAG)1→2 | 88.6% | coding (399/1353 nt) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| JC | 3,676,833 | Δ3 bp | 91.2% | intergenic (‑26/+155) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| RA | 3,701,787 | G→A | 5.3% | intergenic (‑722/+189) | dppA ← / ← proK | dipeptide transporter/tRNA‑Pro |
| RA | 3,701,788 | T→A | 5.0% | intergenic (‑723/+188) | dppA ← / ← proK | dipeptide transporter/tRNA‑Pro |
| RA | 3,701,789 | T→C | 4.8% | intergenic (‑724/+187) | dppA ← / ← proK | dipeptide transporter/tRNA‑Pro |
| RA | 3,701,955 | G→A | 4.4% | intergenic (‑890/+21) | dppA ← / ← proK | dipeptide transporter/tRNA‑Pro |
| RA | 3,772,673 | T→A | 12.1% | L87Q (CTA→CAA) | lldR → | dual role activator/repressor for lldPRD operon |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | NA (NA) | 31 (1.340) | 26/268 | 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 | 1045234 = | 19 (0.820) | 28 (1.210) | 23/268 | NT | 70.0% | intergenic (‑34/‑55) | gfcA/insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| ? | CP009273 | = 1973123 | 5 (0.220) | intergenic (‑669/‑111) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 1203246 = | 3 (0.130) | 12 (0.590) | 12/236 | NT | 83.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 2 (0.100) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 3 (0.130) | 22 (1.080) | 18/236 | NT | 90.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 2 (0.100) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1973115 = | 5 (0.220) | 16 (0.690) | 14/268 | NT | 76.2% | intergenic (‑661/‑119) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2096424 | NA (NA) | 29 (1.250) | 24/268 | NT | 74.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | = 2427745 | 10 (0.430) | coding (476/660 nt) | dedA | DedA family inner membrane protein | |||||
| * | ? | CP009273 | 2282398 = | NA (NA) | 20 (0.860) | 19/268 | NT | 66.7% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 2400257 = | 10 (0.430) | intergenic (‑137/‑783) | lrhA/alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 | |||||
| * | ? | CP009273 | 2282398 = | NA (NA) | 5 (0.220) | 5/266 | NT | 31.2% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 3178254 = | 11 (0.480) | coding (56/291 nt) | yqiC | BMFP family putative fusogenic protein | |||||
| * | ? | CP009273 | = 4572954 | 15 (0.650) | 4 (0.180) | 4/256 | NT | 19.4% | intergenic (‑89/+112) | hsdM/hsdR | DNA methyltransferase M/pseudogene, premature stop codon, host restriction; endonuclease R |
| ? | CP009273 | = 4573041 | 19 (0.860) | intergenic (‑176/+25) | hsdM/hsdR | DNA methyltransferase M/pseudogene, premature stop codon, host restriction; endonuclease R | |||||