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 | 68,504 | T→G | 10.8% | L223V (TTG→GTG) | yabI → | DedA family inner membrane protein |
| RA | 277,680 | C→A | 13.3% | M5I (ATG→ATT) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 295,695 | T→G | 5.1% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 418,994 | C→G | 9.8% | L341V (CTG→GTG) ‡ | malZ → | maltodextrin glucosidase |
| RA | 418,995 | T→G | 12.8% | L341R (CTG→CGG) ‡ | malZ → | maltodextrin glucosidase |
| RA | 763,405 | G→T | 9.0% | V656L (GTA→TTA) | mngA → | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 772,664 | A→C | 7.4% | K289N (AAA→AAC) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
| RA | 777,175 | A→T | 5.6% | intergenic (+67/‑366) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| RA | 838,676 | G→C | 9.8% | D297H (GAC→CAC) | rlmF → | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| RA | 838,711 | T→G | 9.1% | R308R (CGT→CGG) *742Y (TAA→TAC) |
rlmF → ybiO ← |
23S rRNA m(6)A1618 methyltransferase, SAM‑dependent mechanosensitive channel protein, intermediate conductance |
| RA | 859,422 | A→C | 6.5% | T109P (ACC→CCC) | fsaA → | fructose‑6‑phosphate aldolase 1 |
| RA | 910,671 | T→G | 5.5% | intergenic (‑358/+137) | 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 | 1,160,027 | A→C | 11.2% | K159N (AAA→AAC) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,282,287 | T→G | 8.4% | intergenic (+305/+235) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,493 | C→G | 6.4% | intergenic (+511/+29) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,615 | T→G | 8.6% | noncoding (78/171 nt) Q6H (CAA→CAC) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,282,643 | A→C | 6.7% | noncoding (50/171 nt) | rttR ← | rtT sRNA, processed from tyrT transcript |
| RA | 1,385,975 | C→A | 5.1% | V46F (GTT→TTT) | ycjY ← | S9 homolog non‑peptidase family protein |
| RA | 1,828,729 | A→C | 9.2% | E119D (GAA→GAC) | ydjY → | putative ferrodoxin‑like lipoprotein |
| 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 | 2,170,713 | C→A | 15.4% | 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 | 13.4% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,749 | G→T | 5.5% | intergenic (‑66/+242) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,758 | C→A | 5.1% | intergenic (‑75/+233) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,200,977 | T→G | 5.2% | L602V (TTA→GTA) | yehM → | uncharacterized protein |
| RA | 2,222,656 | A→C | 9.1% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,475,229 | C→A | 10.4% | A143S (GCT→TCT) | emrY ← | putative multidrug efflux system |
| RA | 2,514,707 | A→C | 9.0% | intergenic (+20/+245) | lysV → / ← xapR | tRNA‑Lys/transcriptional activator of xapAB |
| RA | 2,719,191 | G→T | 11.2% | intergenic (‑86/+237) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,998,305 | G→T | 16.9% | Q281K (CAA→AAA) | ygeV ← | putative sigma‑54‑interacting transcriptional activator |
| RA | 2,998,344 | G→T | 9.1% | H268N (CAT→AAT) | ygeV ← | putative sigma‑54‑interacting transcriptional activator |
| RA | 3,119,692 | T→G | 10.6% | T64P (ACC→CCC) | glcE ← | glycolate oxidase FAD binding subunit |
| RA | 3,256,876 | A→C | 5.5% | N48K (AAT→AAG) | tdcD ← | propionate kinase/acetate kinase C, anaerobic |
| RA | 3,384,766 | A→C | 6.7% | F208V (TTT→GTT) | tldD ← | putative peptidase |
| RA | 3,449,072 | G→T | 9.4% | G46* (GGA→TGA) | gspC → | general secretory pathway component, cryptic |
| RA | 3,449,080 | C→A | 5.2% | I48I (ATC→ATA) | gspC → | general secretory pathway component, cryptic |
| RA | 3,498,220 | T→G | 9.2% | intergenic (+78/+74) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,498,226 | T→G | 8.8% | intergenic (+84/+68) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,525,235 | C→A | 5.9% | T188T (ACG→ACT) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,546,300 | G→T | 6.1% | intergenic (‑468/‑144) | malP ← / → malT | maltodextrin phosphorylase/mal regulon transcriptional activator |
| RA | 3,602,055 | C→G | 9.0% | intergenic (+46/+56) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,602,063 | A→T | 13.7% | intergenic (+54/+48) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,666,053 | T→G | 5.6% | L94V (TTA→GTA) | yhjC → | LysR family putative transcriptional regulator |
| RA | 3,822,340 | A→C | 18.0% | 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 | 3,901,866 | C→G | 5.8% | intergenic (‑140/+43) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
| RA | 3,901,867 | T→G | 6.8% | intergenic (‑141/+42) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
| RA | 3,901,886 | A→C | 7.8% | intergenic (‑160/+23) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
| RA | 3,991,416 | T→G | 7.3% | L25R (CTT→CGT) | uvrD → | DNA‑dependent ATPase I and helicase II |
| RA | 4,058,518 | C→A | 7.9% | M203I (ATG→ATT) | yihO ← | putative transporter |
| RA | 4,058,521 | C→A | 7.7% | M202I (ATG→ATT) | yihO ← | putative transporter |
| RA | 4,058,564 | G→C | 5.2% | A188G (GCC→GGC) | yihO ← | putative transporter |
| RA | 4,172,827 | C→G | 33.9% | P552R (CCG→CGG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,173,025 | A→T | 17.0% | Q618L (CAG→CTG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,173,034 | C→T | 5.1% | S621F (TCC→TTC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,178,500 | C→T | 23.8% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,402,640 | A→T | 5.2% | E146V (GAG→GTG) | yjfM → | DUF1190 family protein |
| RA | 4,489,321 | C→A | 7.3% | intergenic (+4/+89) | insD1 → / ← yjgX | IS2 transposase TnpB/pseudogene fragment |
| RA | 4,586,640 | A→C | 6.9% | E278D (GAA→GAC) | yjjN → | L‑galactonate oxidoreductase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 454315 | 456692 | 2378 | 150 [130] | [115] 145 | [lon] | [lon] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 439 (0.970) | 454 (1.010) | 73/248 | NT | 50.8% | 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 = | 203 (0.450) | 307 (0.780) | 68/216 | NT | 65.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 144 (0.370) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 202 (0.450) | 330 (0.840) | 58/216 | NT | 67.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 144 (0.370) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 4532499 = | 63 (0.140) | 34 (0.080) | 19/230 | NT | 18.7% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 238 (0.570) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 4532507 | 56 (0.120) | 58 (0.140) | 23/230 | NT | 28.6% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 238 (0.570) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||