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 | 17,872 | A→C | 13.5% | K243N (AAA→AAC) | dacA → | D‑alanyl‑D‑alanine carboxypeptidase |
| RA | 68,857 | G→T | 5.1% | intergenic (+16/‑2) | yabQ → / → divIC | spore cortex biosynthesis protein YabQ/cell division protein DivIC |
| RA | 112,586 | G→T | 6.9% | intergenic (+264/‑40) | gltX → / → cysE | glutamate‑‑tRNA ligase/serine O‑acetyltransferase |
| RA | 131,088 | C→A | 100% | S194Y (TCT→TAT) | fusA → | elongation factor G |
| RA | 135,117 | G→T | 6.8% | intergenic (+164/‑74) | EO946_RS00715 → / → rpsJ | alpha/beta hydrolase/30S ribosomal protein S10 |
| RA | 138,085 | C→A | 5.5% | I19I (ATC→ATA) | rpsS → | 30S ribosomal protein S19 |
| RA | 177,067 | C→G | 10.2% | intergenic (+240/‑32) | EO946_RS01020 → / → EO946_RS01025 | alcohol dehydrogenase/SulP family inorganic anion transporter |
| RA | 314,425 | T→G | 5.4% | L83R (CTT→CGT) | niaP → | niacin permease NiaP |
| RA | 316,256 | G→C | 5.4% | A26P (GCA→CCA) | opuAA → | glycine/proline betaine ABC transporter ATP‑binding protein OpuAA |
| RA | 316,262 | C→A | 7.5% | Q28K (CAA→AAA) | opuAA → | glycine/proline betaine ABC transporter ATP‑binding protein OpuAA |
| RA | 361,352 | T→A | 9.3% | M147K (ATG→AAG) | EO946_RS01960 → | FAD/NAD(P)‑binding protein |
| RA | 376,966 | A→C | 6.6% | K781T (AAA→ACA) | srfAA → | surfactin non‑ribosomal peptide synthetase SrfAA |
| RA | 438,792 | C→A | 8.1% | intergenic (‑58/‑48) | gabR ← / → gabT | transcriptional regulator GabR/4‑aminobutyrate‑‑2‑oxoglutarate transaminase |
| RA | 549,119 | T→G | 14.4% | L44R (CTG→CGG) | EO946_RS02865 → | PLP‑dependent aminotransferase family protein |
| RA | 549,144 | A→C | 16.3% | Q52H (CAA→CAC) | EO946_RS02865 → | PLP‑dependent aminotransferase family protein |
| RA | 607,359 | A→C | 15.2% | T68P (ACC→CCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,413 | A→C | 6.3% | T86P (ACC→CCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,494 | A→C | 5.4% | T113P (ACC→CCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,514 | T→G | 5.1% | A119A (GCT→GCG) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,592 | A→C | 13.5% | E145D (GAA→GAC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,594 | C→T | 9.9% | A146V (GCC→GTC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,638 | G→C | 8.1% | A161P (GCC→CCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,663 | A→C | 5.4% | E169A (GAA→GCA) ‡ | EO946_RS03185 → | collagen‑like protein |
| RA | 607,664 | A→C | 5.9% | E169D (GAA→GAC) ‡ | EO946_RS03185 → | collagen‑like protein |
| RA | 607,665 | G→C | 5.2% | A170P (GCC→CCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,783 | T→C | 5.1% | V209A (GTC→GCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 634,052 | T→G | 14.3% | E573D (GAA→GAC) | EO946_RS03330 ← | ABC‑F family ATP‑binding cassette domain‑containing protein |
| RA | 634,089 | C→A | 5.0% | R561L (CGT→CTT) | EO946_RS03330 ← | ABC‑F family ATP‑binding cassette domain‑containing protein |
| RA | 755,531 | A→C | 10.8% | Q22H (CAA→CAC) | EO946_RS03880 → | rhamnogalacturonan acetylesterase |
| RA | 762,385 | T→G | 7.4% | intergenic (+17/‑38) | EO946_RS03895 → / → EO946_RS03900 | extracellular solute‑binding protein/sugar ABC transporter permease |
| RA | 803,252 | G→T | 7.9% | S37R (AGC→AGA) | yfmC ← | Fe(3+)‑citrate ABC transporter substrate‑binding protein YfmC |
| RA | 896,727 | C→A | 5.6% | H99N (CAT→AAT) | recX → | recombination regulator RecX |
| RA | 986,801 | G→T | 12.0% | D372Y (GAT→TAT) | spoVR → | stage V sporulation protein SpoVR |
| RA | 1,014,046 | G→T | 10.1% | A44E (GCA→GAA) | EO946_RS05230 ← | polysaccharide deacetylase |
| RA | 1,036,330 | G→T | 6.8% | E59* (GAA→TAA) | EO946_RS05355 → | ABC transporter permease |
| RA | 1,097,451 | C→A | 8.7% | P65Q (CCA→CAA) | EO946_RS05675 → | MarR family transcriptional regulator |
| RA | 1,111,632 | T→G | 10.0% | L576R (CTT→CGT) | addB → | helicase‑exonuclease AddAB subunit AddB |
| RA | 1,111,675 | C→G | 8.9% | V590V (GTC→GTG) | addB → | helicase‑exonuclease AddAB subunit AddB |
| RA | 1,111,684 | G→T | 8.0% | M593I (ATG→ATT) | addB → | helicase‑exonuclease AddAB subunit AddB |
| RA | 1,151,987 | G→T | 6.7% | V72V (GTC→GTA) | EO946_RS05920 ← | GNAT family N‑acetyltransferase |
| RA | 1,152,007 | G→C | 7.8% | L66V (CTT→GTT) | EO946_RS05920 ← | GNAT family N‑acetyltransferase |
| RA | 1,263,949 | G→T | 6.1% | R79R (CGA→AGA) | fetB ← | iron export ABC transporter permease subunit FetB |
| RA | 1,293,314 | C→T | 5.2% | C129C (TGC→TGT) | EO946_RS06740 → | sigma‑70 family RNA polymerase sigma factor |
| RA | 1,512,548 | A→T | 5.7% | intergenic (‑76/‑37) | EO946_RS07905 ← / → typA | YlaF family protein/translational GTPase TypA |
| RA | 1,514,854 | T→G | 12.0% | intergenic (+58/+1) | EO946_RS07915 → / ← EO946_RS07920 | YlaH‑like family protein/YlaI family protein |
| RA | 1,514,935 | G→T | 5.1% | Q44K (CAA→AAA) | EO946_RS07920 ← | YlaI family protein |
| RA | 1,582,930 | C→A | 9.9% | H41N (CAT→AAT) | ylyA → | sporulation‑related RNA polymerase‑binding protein YlyA |
| RA | 1,591,355 | T→G | 11.1% | W360G (TGG→GGG) | carB → | carbamoyl‑phosphate synthase (glutamine‑hydrolyzing) large subunit |
| RA | 1,642,832 | C→T | 100% | P128L (CCT→CTT) | rimM → | ribosome maturation factor RimM |
| RA | 1,669,737 | C→T | 100% | Q88* (CAG→TAG) | fliM → | flagellar motor switch protein FliM |
| RA | 1,800,874 | A→C | 9.2% | S3519R (AGC→CGC) | EO946_RS09135 → | SDR family NAD(P)‑dependent oxidoreductase |
| RA | 1,936,589 | T→G | 10.8% | K3554N (AAA→AAC) | EO946_RS09735 ← | non‑ribosomal peptide synthetase |
| RA | 2,169,199 | C→G | 100% | G81G (GGG→GGC) | EO946_RS10950 ← | class I SAM‑dependent methyltransferase |
| RA | 2,237,227 | C→A | 6.0% | intergenic (‑334/+15) | EO946_RS11350 ← / ← aroA | tetratricopeptide repeat protein/3‑phosphoshikimate 1‑carboxyvinyltransferase |
| RA | 2,270,052 | G→C | 14.4% | L43V (CTT→GTT) | prsW ← | glutamic‑type intramembrane protease PrsW |
| RA | 2,350,843 | T→G | 6.3% | pseudogene (938/1182 nt) | EO946_RS12020 ← | IS3 family transposase |
| RA | 2,387,026 | T→G | 19.9% | K367T (AAG→ACG) | EO946_RS12195 ← | acetyl‑CoA C‑acetyltransferase |
| RA | 2,387,114 | C→A | 8.2% | V338L (GTA→TTA) | EO946_RS12195 ← | acetyl‑CoA C‑acetyltransferase |
| RA | 2,502,242 | T→G | 20.0% | T274P (ACG→CCG) | hrcA ← | heat‑inducible transcriptional repressor HrcA |
| RA | 2,678,408 | G→T | 6.5% | F333L (TTC→TTA) | ysxE ← | spore coat protein YsxE |
| RA | 2,812,782 | T→G | 8.0% | K202T (AAG→ACG) | EO946_RS14520 ← | SDR family oxidoreductase |
| RA | 2,830,550 | G→T | 12.9% | A98S (GCA→TCA) | brnQ → | branched‑chain amino acid transport system II carrier protein |
| RA | 2,901,671 | A→C | 13.5% | K411T (AAA→ACA) | EO946_RS14945 → | extracellular solute‑binding protein |
| RA | 2,979,248 | T→C | 23.7% | noncoding (1553/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,980,160 | G→A | 29.2% | noncoding (641/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,991,227 | T→G | 24.4% | intergenic (+28/‑179) | gbsR → / → bslA | transcriptional regulator GbsR/biofilm‑surface layer protein BslA |
| RA | 3,184,761 | T→G | 5.5% | R122R (AGG→CGG) | EO946_RS16485 ← | tautomerase family protein |
| MC JC | 3,191,671 | (ATTATAATT)2→1 | 100% | intergenic (+3/‑66) | EO946_RS16520 → / → mrgA | oxidoreductase/metalloregulation DNA‑binding stress protein MgrA |
| RA | 3,193,442 | T→G | 6.6% | E61D (GAA→GAC) | htrB ← | serine protease Do‑like protein HtrB |
| RA | 3,280,377 | G→T | 12.4% | Q115K (CAA→AAA) | EO946_RS16965 ← | lantibiotic dehydratase |
| RA | 3,285,491 | T→C | 5.5% | I304V (ATT→GTT) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,567 | C→T | 32.6% | L278L (CTG→CTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,575 | T→G | 32.9% | N276H (AAT→CAT) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,580 | A→G | 35.4% | I274T (ATA→ACA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,647 | C→A | 38.9% | V252L (GTA→TTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,713 | G→A | 31.1% | L230L (CTA→TTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,319,761 | T→G | 5.0% | pseudogene (544/1292 nt) | EO946_RS17170 ← | arabinogalactan endo‑beta‑1,4‑galactanase |
| RA | 3,349,666 | T→G | 5.7% | intergenic (+1/+26) | EO946_RS17305 → / ← padC | hypothetical protein/phenolic acid decarboxylase |
| RA | 3,362,393 | G→C | 8.4% | L99L (CTG→CTC) | EO946_RS17380 → | MazG‑like family protein |
| RA | 3,394,360 | T→G | 11.3% | K180N (AAA→AAC) | ppaX ← | pyrophosphatase PpaX |
| RA | 3,446,962 | C→A | 13.7% | M208I (ATG→ATT) | degU ← | two‑component system response regulator DegU |
| RA | 3,446,970 | G→T | 17.7% | Q206K (CAA→AAA) | degU ← | two‑component system response regulator DegU |
| RA | 3,447,038 | T→G | 11.6% | N183T (AAC→ACC) | degU ← | two‑component system response regulator DegU |
| RA | 3,496,384 | G→T | 5.4% | I348I (ATC→ATA) | EO946_RS17995 ← | glucosaminidase domain‑containing protein |
| RA | 3,498,775 | C→A | 6.4% | Q2K (CAA→AAA) | EO946_RS18005 → | spore germination protein |
| RA | 3,511,851 | T→G | 7.0% | Y156D (TAT→GAT) | EO946_RS18060 → | LacI family transcriptional regulator |
| RA | 3,539,642 | A→C | 5.1% | L104R (CTG→CGG) | EO946_RS18215 ← | T7SS effector LXG polymorphic toxin |
| RA | 3,561,985 | G→C | 15.0% | intergenic (‑631/‑167) | EO946_RS18300 ← / → EO946_RS21105 | response regulator/HAMP domain‑containing histidine kinase |
| RA | 3,562,015 | A→C | 12.1% | intergenic (‑661/‑137) | EO946_RS18300 ← / → EO946_RS21105 | response regulator/HAMP domain‑containing histidine kinase |
| RA | 3,569,139 | C→T | 100% | M166I (ATG→ATA) | mbl ← | cell shape‑determining protein Mbl |
| RA | 3,569,289 | T→G | 7.4% | E116D (GAA→GAC) | mbl ← | cell shape‑determining protein Mbl |
| RA | 3,584,358 | C→A | 6.0% | L347I (CTA→ATA) | EO946_RS18420 → | N‑acetylneuraminate synthase family protein |
| RA | 3,635,976 | C→T | 100% | A174T (GCA→ACA) | EO946_RS18730 ← | fructose‑bisphosphate aldolase |
| RA | 3,719,864 | T→G | 7.6% | S79R (AGC→CGC) | EO946_RS19145 ← | YwdI family protein |
| RA | 3,746,962 | C→A | 5.2% | D36Y (GAT→TAT) | EO946_RS19275 ← | galactokinase |
| RA | 3,851,234 | C→A | 5.4% | M47I (ATG→ATT) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,851,237 | G→T | 8.3% | I46I (ATC→ATA) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,851,254 | G→C | 8.9% | L41V (CTT→GTT) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,945,908 | T→G | 6.6% | L388R (CTT→CGT) | EO946_RS20305 → | Na+/H+ antiporter |
| RA | 3,946,821 | T→G | 6.2% | E191A (GAG→GCG) | EO946_RS20310 ← | polysaccharide pyruvyl transferase family protein |
| RA | 3,976,114 | G→T | 6.7% | A31E (GCA→GAA) | rlmH ← | 23S rRNA (pseudouridine(1915)‑N(3))‑methyltransferase RlmH |
| RA | 3,976,145 | C→A | 5.4% | E21* (GAA→TAA) | rlmH ← | 23S rRNA (pseudouridine(1915)‑N(3))‑methyltransferase RlmH |
| RA | 3,976,149 | G→T | 7.1% | G19G (GGC→GGA) | rlmH ← | 23S rRNA (pseudouridine(1915)‑N(3))‑methyltransferase RlmH |
| RA | 3,996,857 | C→A | 7.2% | intergenic (‑163/+43) | purA ← / ← EO946_RS20530 | adenylosuccinate synthase/VOC family protein |
| RA | 3,996,891 | G→T | 5.8% | intergenic (‑197/+9) | purA ← / ← EO946_RS20530 | adenylosuccinate synthase/VOC family protein |
| RA | 4,000,069 | C→A | 5.7% | F105L (TTC→TTA) | EO946_RS20555 → | MFS transporter |
| RA | 4,000,117 | G→T | 5.1% | L121F (TTG→TTT) | EO946_RS20555 → | MFS transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP034943 | = 91969 | NA (NA) | 15 (0.030) | 12/250 | NT | NA | intergenic (+131/‑39) | EO946_RS00485/EO946_RS00490 | 16S ribosomal RNA/23S ribosomal RNA |
| ? | NZ_CP034943 | 91973 = | NA (NA) | intergenic (+135/‑35) | EO946_RS00485/EO946_RS00490 | 16S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | NZ_CP034943 | = 607225 | 485 (1.050) | 28 (0.070) +AGGGGCTACTGGGGACGT |
10/216 | NT | 7.8% | coding (68/1125 nt) | EO946_RS03185 | collagen‑like protein |
| ? | NZ_CP034943 | 607703 = | 284 (0.610) | coding (546/1125 nt) | EO946_RS03185 | collagen‑like protein | |||||
| * | ? | NZ_CP034943 | 607566 = | 284 (0.610) | 148 (0.320) | 35/248 | NT | 25.0% | coding (409/1125 nt) | EO946_RS03185 | collagen‑like protein |
| ? | NZ_CP034943 | = 607835 | 609 (1.340) | coding (678/1125 nt) | EO946_RS03185 | collagen‑like protein | |||||