mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 104,041 | G→T | 21.7% | intergenic (+80/‑151) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 148,177 | G→T | 8.7% | T181N (ACC→AAC) | yadL ← | putative fimbrial‑like adhesin protein |
| RA | 148,221 | A→C | 10.3% | V166V (GTT→GTG) | yadL ← | putative fimbrial‑like adhesin protein |
| RA | 161,068 | A→C | 29.3% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 221,455 | G→A | 5.5% | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,476 | A→T | 5.0% | noncoding (1219/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 277,654 | G→C | 5.6% | S14* (TCA→TGA) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 277,676 | A→C | 5.3% | W7G (TGG→GGG) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 298,180 | T→G | 7.5% | T35T (ACA→ACC) | paoA ← | PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit |
| RA | 503,882 | G→T | 8.6% | W70L (TGG→TTG) | ybaQ → | putative DNA‑binding transcriptional regulator |
| RA | 513,790 | T→G | 5.3% | intergenic (‑55/+6) | ybbN ← / ← ybbO | DnaK co‑chaperone, thioredoxin‑like protein/putative oxidoreductase |
| RA | 620,047 | T→G | 7.3% | intergenic (‑81/‑294) | fepB ← / → entC | iron‑enterobactin transporter subunit/isochorismate synthase 1 |
| RA | 838,735 | T→G | 5.8% | L734F (TTA→TTC) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 910,669 | A→T | 13.4% | intergenic (‑356/+139) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 910,671 | T→G | 6.5% | intergenic (‑358/+137) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 910,682 | T→G | 8.7% | intergenic (‑369/+126) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 1,016,418 | C→A | 100% | intergenic (‑43/‑176) | sulA ← / → sxy | SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor |
| RA | 1,282,287 | T→G | 5.3% | intergenic (+305/+235) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,345,477 | T→A | 7.8% | intergenic (‑181/+187) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,345,485 | G→C | 5.3% | intergenic (‑189/+179) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,345,502 | T→G | 5.1% | intergenic (‑206/+162) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,683,030 | A→C | 6.5% | K66N (AAA→AAC) | manA → | mannose‑6‑phosphate isomerase |
| RA | 1,896,745 | A→C | 10.1% | K147N (AAA→AAC) | manX → | fused mannose‑specific PTS enzymes: IIA component/IIB component |
| JC JC | 1,972,762 | IS5 (–) +4 bp | 100% | intergenic (‑308/‑469) | flhD ← / → uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| RA | 2,170,707 | C→A | 12.4% | intergenic (‑24/+284) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,713 | C→A | 12.9% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,724 | G→T | 20.3% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,746 | C→A | 16.2% | intergenic (‑63/+245) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,758 | C→A | 10.6% | intergenic (‑75/+233) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,775 | G→T | 9.8% | intergenic (‑92/+216) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,404,713 | C→A | 5.0% | S40I (AGC→ATC) | yfbS ← | putative transporter |
| RA | 2,404,729 | C→A | 9.2% | V35F (GTC→TTC) | yfbS ← | putative transporter |
| RA | 2,632,621 | T→G | 7.5% | N8H (AAC→CAC) | yfgM ← | putative anti‑RcsB factor |
| RA | 2,719,149 | T→G | 9.5% | intergenic (‑44/+279) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,719,209 | T→A | 6.9% | intergenic (‑104/+219) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,958,473 | T→G | 6.0% | E14D (GAA→GAC) | thyA ← | thymidylate synthetase |
| RA | 3,039,427 | T→A | 7.3% | intergenic (‑167/+100) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex |
| RA | 3,048,273 | A→T | 6.4% | T177T (ACT→ACA) | ygfB ← | UPF0149 family protein |
| RA | 3,256,881 | C→A | 6.3% | V47L (GTA→TTA) | tdcD ← | propionate kinase/acetate kinase C, anaerobic |
| RA | 3,384,766 | A→C | 7.3% | F208V (TTT→GTT) | tldD ← | putative peptidase |
| RA | 3,385,651 | C→G | 5.2% | intergenic (‑264/+166) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,525,250 | C→A | 5.2% | W183C (TGG→TGT) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,602,075 | A→C | 9.9% | intergenic (+66/+36) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,602,081 | A→C | 6.8% | intergenic (+72/+30) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,822,340 | A→C | 13.3% | Q12H (CAA→CAC) | xanP → | xanthine permease |
| RA | 3,888,770 | A→G | 100% | I400I (ATT→ATC) | purP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,896,104 | G→T | 5.5% | L320M (CTG→ATG) | bglB ← | cryptic phospho‑beta‑glucosidase B |
| RA | 3,901,867 | T→G | 5.7% | intergenic (‑141/+42) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
| RA | 4,058,521 | C→A | 5.1% | M202I (ATG→ATT) | yihO ← | putative transporter |
| RA | 4,178,500 | C→T | 100% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,375,441 | C→G | 5.4% | L78V (CTG→GTG) | yjeN → | uncharacterized protein |
| RA | 4,467,839 | A→C | 7.2% | L97R (CTT→CGT) | argI ← | ornithine carbamoyltransferase 1 |
| RA | 4,586,638 | G→C | 13.9% | E278Q (GAA→CAA) | yjjN → | L‑galactonate oxidoreductase |
| RA | 4,598,183 | T→G | 5.5% | L61R (CTG→CGG) | rimI → | ribosomal‑protein‑S18‑alanine N‑acetyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 454284 | 456690 | 2407 | 148 [142] | [126] 154 | [lon] | [lon] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 398 (0.980) | 326 (0.810) | 73/250 | NT | 45.0% | 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 = | 265 (0.650) | 166 (0.470) | 53/218 | NT | 45.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 173 (0.490) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 252 (0.620) | 153 (0.430) | 43/218 | NT | 43.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 173 (0.490) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 4532499 = | 73 (0.180) | 34 (0.090) | 17/232 | NT | 21.1% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 186 (0.500) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 4532507 | 81 (0.200) | 51 (0.140) | 23/232 | NT | 28.1% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 186 (0.500) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||