mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 31,729 | T→G | 9.8% | S305A (TCC→GCC) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 31,745 | T→G | 6.4% | L310R (CTG→CGG) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 68,486 | T→G | 15.8% | L217V (TTG→GTG) | yabI → | DedA family inner membrane protein |
| RA | 104,042 | A→T | 22.6% | intergenic (+81/‑150) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 148,221 | A→C | 14.6% | V166V (GTT→GTG) | yadL ← | putative fimbrial‑like adhesin protein |
| RA | 161,068 | A→C | 24.1% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 161,082 | T→G | 18.0% | intergenic (+61/‑135) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 221,425 | T→C | 5.3% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 5.7% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,464 | G→C | 5.1% | noncoding (1207/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 277,676 | A→C | 8.7% | W7G (TGG→GGG) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 418,994 | C→G | 7.7% | L341V (CTG→GTG) ‡ | malZ → | maltodextrin glucosidase |
| RA | 418,995 | T→G | 9.3% | L341R (CTG→CGG) ‡ | malZ → | maltodextrin glucosidase |
| RA | 445,212 | C→T | 100% | G296S (GGT→AGT) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 513,790 | T→G | 7.0% | intergenic (‑55/+6) | ybbN ← / ← ybbO | DnaK co‑chaperone, thioredoxin‑like protein/putative oxidoreductase |
| RA | 513,803 | T→G | 6.1% | Q268P (CAG→CCG) | ybbO ← | putative oxidoreductase |
| RA | 620,060 | A→C | 7.2% | intergenic (‑94/‑281) | fepB ← / → entC | iron‑enterobactin transporter subunit/isochorismate synthase 1 |
| RA | 772,664 | A→C | 11.1% | K289N (AAA→AAC) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
| RA | 780,417 | G→T | 10.0% | T119T (ACC→ACA) | ybgS ← | putative periplasmic protein |
| RA | 838,652 | T→G | 21.1% | F289V (TTT→GTT) | rlmF → | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| RA | 859,422 | A→C | 6.0% | T109P (ACC→CCC) | fsaA → | fructose‑6‑phosphate aldolase 1 |
| RA | 910,671 | T→G | 9.7% | intergenic (‑358/+137) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 1,147,344 | T→G | 7.5% | intergenic (+37/‑51) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,147,345 | T→G | 10.9% | intergenic (+38/‑50) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,147,346 | T→G | 10.1% | intergenic (+39/‑49) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,160,001 | G→T | 5.6% | D151Y (GAT→TAT) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,160,010 | C→A | 7.3% | H154N (CAT→AAT) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,160,015 | A→C | 13.0% | E155D (GAA→GAC) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,160,024 | G→C | 21.0% | M158I (ATG→ATC) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,160,027 | A→C | 11.4% | K159N (AAA→AAC) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,288,276 | C→A | 100% | V35F (GTT→TTT) | hns ← | global DNA‑binding transcriptional dual regulator H‑NS |
| RA | 1,345,477 | T→A | 9.5% | intergenic (‑181/+187) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,356,115 | C→A | 5.6% | H247N (CAT→AAT) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,815,273 | G→T | 12.3% | R67S (CGC→AGC) | chbC ← | N,N'‑diacetylchitobiose‑specific enzyme IIC component of PTS |
| RA | 1,999,170 | T→G | 13.1% | P129P (CCT→CCG) | fliS → | flagellar protein potentiates polymerization |
| RA | 2,156,363 | T→G | 5.3% | F3V (TTC→GTC) | baeS → | sensory histidine kinase in two‑component regulatory system with BaeR |
| RA | 2,170,713 | C→A | 14.5% | 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 | 13.7% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,178,966 | C→A | 6.6% | intergenic (‑186/+37) | thiM ← / ← rcnR | hydoxyethylthiazole kinase/transcriptional repressor of rcnA |
| RA | 2,200,977 | T→G | 5.5% | L602V (TTA→GTA) | yehM → | uncharacterized protein |
| RA | 2,222,656 | A→C | 8.0% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,463,906 | C→A | 30.6% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,463,930 | G→T | 7.5% | V441L (GTA→TTA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,632,621 | T→G | 10.7% | N8H (AAC→CAC) | yfgM ← | putative anti‑RcsB factor |
| RA | 2,646,494 | A→C | 8.1% | K214N (AAA→AAC) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,998,364 | G→T | 7.0% | A261E (GCA→GAA) | ygeV ← | putative sigma‑54‑interacting transcriptional activator |
| RA | 3,048,247 | A→T | 7.5% | V186E (GTA→GAA) | ygfB ← | UPF0149 family protein |
| RA | 3,072,806 | A→G | 100% | intergenic (‑117/+197) | cmtB ← / ← tktA | putative mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamine triphosphate‑binding |
| RA | 3,119,715 | T→G | 5.9% | Y56S (TAC→TCC) | glcE ← | glycolate oxidase FAD binding subunit |
| RA | 3,232,989 | A→T | 6.5% | intergenic (+85/‑314) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,434,282 | C→A | 34.1% | G36V (GGC→GTC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,533,053 | C→A | 5.2% | G770G (GGC→GGA) | yhgF → | putative transcriptional accessory protein |
| RA | 3,546,300 | G→T | 6.2% | intergenic (‑468/‑144) | malP ← / → malT | maltodextrin phosphorylase/mal regulon transcriptional activator |
| RA | 3,602,069 | A→C | 6.3% | intergenic (+60/+42) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,602,079 | G→C | 6.9% | intergenic (+70/+32) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,721,469 | A→C | 5.5% | D421E (GAT→GAG) | xylB ← | xylulokinase |
| RA | 3,721,480 | T→G | 6.3% | T418P (ACG→CCG) | xylB ← | xylulokinase |
| RA | 3,822,340 | A→C | 9.7% | Q12H (CAA→CAC) | xanP → | xanthine permease |
| RA | 3,901,867 | T→G | 8.9% | intergenic (‑141/+42) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
| RA | 3,901,886 | A→C | 8.6% | intergenic (‑160/+23) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
| RA | 3,997,345 | G→T | 6.4% | T65K (ACG→AAG) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,028,635 | A→G | 6.5% | intergenic (+122/‑256) | hemG → / → rrsA | protoporphyrin oxidase, flavoprotein/16S ribosomal RNA of rrnA operon |
| RA | 4,178,209 | C→T | 5.0% | R978C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,500 | C→T | 9.7% | R1075C (CGT→TGT) ‡ | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,501 | G→T | 37.8% | R1075L (CGT→CTT) ‡ | rpoC → | RNA polymerase, beta prime subunit |
| JC | 4,178,880 | +GAACGTGTA | 17.5% | coding (3603/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,234,527 | C→G | 9.6% | L159L (CTG→CTC) | malF ← | maltose transporter subunit |
| RA | 4,402,667 | C→G | 8.7% | S155C (TCC→TGC) | yjfM → | DUF1190 family protein |
| RA | 4,561,269 | G→A | 100% | S41S (AGC→AGT) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 4323057 | 4323805 | 749 | 159 [151] | [147] 167 | [basS]–[eptA] | [basS],basR,[eptA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 318 (0.740) | 451 (1.050) | 80/250 | NT | 58.6% | 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 = | 254 (0.590) | 232 (0.620) | 65/218 | NT | 57.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 126 (0.340) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 248 (0.580) | 264 (0.700) | 48/218 | NT | 60.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 126 (0.340) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 2282398 = | NA (NA) | 82 (0.190) | 28/250 | NT | 20.0% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 2766540 = | 327 (0.760) | pseudogene (2/117 nt) | yfjV | pseudogene, CP4‑57 prophage;Phage or Prophage Related; putative pump protein | |||||
| * | ? | CP009273 | = 2766544 | 304 (0.710) | 97 (0.230) | 38/248 | NT | 24.3% | intergenic (‑3/‑133) | yfjV/yfjW | pseudogene, CP4‑57 prophage;Phage or Prophage Related; putative pump protein/CP4‑57 prophage; putative inner membrane protein |
| ? | CP009273 | 3123506 = | NA (NA) | intergenic (‑4/‑31) | yghO/insH1 | pseudogene, DNA‑binding transcriptional regulator homology/IS5 transposase and trans‑activator | |||||