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 | seq id | position | mutation | annotation | gene | description |
| RA | CP006881 | 30,182 | C→T | intergenic (+147/‑96) | U712_00120 → / → U712_20865 | Sigma‑K factor‑processing regulatory protein BofA/16S ribosomal RNA |
| RA | CP006881 | 53,413 | G→A | intergenic (+45/‑94) | U712_00230 → / → U712_00235 | Protein sspF/4‑diphosphocytidyl‑2‑C‑methyl‑D‑erythritol kinase |
| RA | CP006881 | 214,982 | C→T | A268V (GCC→GTC) | U712_00980 → | Uncharacterized protein skfB |
| RA | CP006881 | 681,397 | A→G | intergenic (‑6/‑103) | U712_03330 ← / → U712_03335 | putative membrane protein yerD/Hypothetical Protein |
| RA | CP006881 | 924,071 | (A)5→6 | intergenic (‑51/‑228) | U712_04490 ← / → U712_04495 | Vegetative catalase/Aliphatic sulfonates import ATP‑binding protein SsuB |
| RA | CP006881 | 1,091,489 | (T)6→7 | coding (1157/1326 nt) | U712_05390 ← | NTD biosynthesis operon protein ntdA |
| RA | CP006881 | 1,256,397 | T→C | P269P (CCT→CCC) | U712_06330 → | putative UDP‑glucosyltransferase yjiC |
| RA | CP006881 | 1,653,712 | G→A | A186T (GCA→ACA) | U712_08495 → | GTP‑sensing transcriptional pleiotropic repressor CodY |
| RA | CP006881 | 1,655,979 | Δ1 bp | coding (431/1596 nt) | U712_08515 → | Flagellar M‑ring protein |
| RA | CP006881 | 1,803,627 | G→T | pseudogene (6260/16546 nt) | U712_09020 → | frameshift (+1) in homopolymer run at nucleotide position 6839 in gene |
| RA | CP006881 | 2,289,100 | G→T | P184T (CCG→ACG) | U712_11585 ← | putative oxidoreductase yqjQ |
| RA | CP006881 | 2,801,996 | G→A | A327T (GCC→ACC) | U712_14440 → | UPF0118 membrane protein ytvI |
| RA | CP006881 | 2,963,948 | G→A | intergenic (‑135/+145) | U712_15285 ← / ← U712_15290 | Manganese‑binding lipoprotein mntA/o‑succinylbenzoate synthase |
| RA | CP006881 | 3,285,264 | (T)7→8 | intergenic (‑84/+136) | U712_16905 ← / ← U712_16910 | Transcriptional repressor sdpR/Glycine betaine/carnitine/choline transport system permease protein opuCD |
| RA | CP006881 | 3,414,697 | A→G | I101V (ATT→GTT) | U712_17535 → | Glucosamine‑6‑phosphate deaminase 1 |
| RA | CP006881 | 3,578,472 | (A)7→6 | intergenic (‑65/‑70) | U712_18365 ← / → U712_18370 | Stage II sporulation protein Q/Putative phosphinothricin acetyltransferase YwnH |
| RA | CP006881 | 3,579,791 | (A)7→6 | coding (79/132 nt) | U712_18380 → | Hypothetical Protein |
| RA | CP006881 | 3,723,022 | G→A | intergenic (‑136/‑165) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,045 | T→C | intergenic (‑159/‑142) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,067 | 1 bp→AT | intergenic (‑181/‑120) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,091 | A→T | intergenic (‑205/‑96) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,095 | T→A | intergenic (‑209/‑92) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,097 | T→G | intergenic (‑211/‑90) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,118 | C→T | intergenic (‑232/‑69) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,121 | T→A | intergenic (‑235/‑66) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,130 | A→T | intergenic (‑244/‑57) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,162 | C→T | intergenic (‑276/‑25) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,166 | C→G | intergenic (‑280/‑21) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,183 | A→G | intergenic (‑297/‑4) | U712_19190 ← / → U712_19195 | PTS system sucrose‑specific EIIBC component/putative transporter ywcJ |
| RA | CP006881 | 3,723,204 | G→A | L6L (TTG→TTA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,210 | A→G | K8K (AAA→AAG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,222 | C→T | Y12Y (TAC→TAT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,231 | C→A | N15K (AAC→AAA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,236 | T→A | L17Q (CTA→CAA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,246 | T→C | F20F (TTT→TTC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,248 | T→C | V21A (GTT→GCT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,252 | T→A | S22S (TCT→TCA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,273 | 2 bp→TC | coding (87‑88/771 nt) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,276 | A→G | R30R (AGA→CGG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,291 | C→T | S35S (AGC→AGT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,294 | G→A | M36I (ATG→ATA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,300 | C→T | I38I (ATC→ATT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,303 | A→T | G39G (GGA→GGT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,306 | C→T | F40F (TTC→TTT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,336 | T→C | S50S (AGT→AGC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,344 | C→T | S53F (TCT→TTT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,351 | G→T | A55A (GCG→GCT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,366 | T→C | A60A (GCT→GCC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,387 | A→T | T67T (ACA→ACT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,406 | C→A | L74M (CTG→ATG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,438 | T→C | T84T (ACT→ACC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,447 | T→C | T87T (ACT→ACC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,459 | T→C | T91T (ACT→ACC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,474 | A→G | R96R (CGA→CGG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,483 | 2 bp→CA | coding (297‑298/771 nt) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,492 | A→C | R102R (CGA→CGC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,501 | G→A | L105L (CTG→CTA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,505 | C→T | L107L (CTG→TTG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,534 | G→A | L116L (TTG→TTA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,549 | A→G | L121L (CTA→CTG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,558 | T→C | I124I (ATT→ATC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,573 | A→G | T129T (ACA→ACG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,576 | G→A | G130G (GGG→GGA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,589 | G→C | A135P (GCT→CCT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,616 | C→T | L144L (CTG→TTG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,642 | C→G | P152P (CCC→CCG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,652 | C→T | L156L (CTG→TTG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,666 | G→A | G160G (GGG→GGA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,717 | T→C | L177L (CTT→CTC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,729 | G→A | G181G (GGG→GGA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,738 | C→T | L184L (CTC→CTT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,771 | C→T | F195F (TTC→TTT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,783 | C→T | F199F (TTC→TTT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,822 | A→G | S212S (TCA→TCG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,853 | G→C | V223M (GTA→CTG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,855 | A→G | V223M (GTA→CTG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,879 | T→C | I231I (ATT→ATC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,888 | A→G | T234T (ACA→ACG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,897 | C→T | N237N (AAC→AAT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,912 | G→A | M242I (ATG→ATA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,915 | C→T | V243V (GTC→GTT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,933 | T→C | Y249Y (TAT→TAC) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,939 | G→A | T251T (ACG→ACA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,942 | C→G | L252L (CTC→CTG) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,948 | C→T | P254P (CCC→CCT) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,723,952 | A→C | K256Q (AAA→CAA) | U712_19195 → | putative transporter ywcJ |
| RA | CP006881 | 3,724,053 | C→T | E258E (GAG→GAA) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,078 | C→T | S250N (AGT→AAT) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,092 | T→C | A245A (GCA→GCG) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,101 | A→C | L242L (CTT→CTG) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,119 | A→G | F236F (TTT→TTC) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,194 | A→G | S211S (AGT→AGC) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,200 | T→C | A209A (GCA→GCG) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,208 | T→G | R207R (AGA→CGA) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,274 | C→T | E185K (GAA→AAA) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,392 | A→C | L145L (CTT→CTG) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,446 | G→A | Y127Y (TAC→TAT) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,467 | T→C | K120K (AAA→AAG) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,542 | A→G | S95S (TCT→TCC) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,587 | C→T | G80G (GGG→GGA) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,623 | A→T | I68I (ATT→ATA) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,659 | A→G | F56F (TTT→TTC) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,678 | T→C | H50R (CAC→CGC) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,719 | G→A | D36D (GAC→GAT) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,749 | T→C | P26P (CCA→CCG) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,808 | G→A | L7L (CTA→TTA) | U712_19200 ← | SacPA operon antiterminator |
| RA | CP006881 | 3,724,831 | C→T | intergenic (‑5/+35) | U712_19200 ← / ← U712_19205 | SacPA operon antiterminator/Uncharacterized protein ywcI |
| RA | CP006881 | 3,724,849 | A→T | intergenic (‑23/+17) | U712_19200 ← / ← U712_19205 | SacPA operon antiterminator/Uncharacterized protein ywcI |
| RA | CP006881 | 3,724,902 | A→C | A89A (GCT→GCG) | U712_19205 ← | Uncharacterized protein ywcI |
| RA | CP006881 | 3,724,977 | T→C | Q64Q (CAA→CAG) | U712_19205 ← | Uncharacterized protein ywcI |
| RA | CP006881 | 3,724,980 | T→C | K63K (AAA→AAG) | U712_19205 ← | Uncharacterized protein ywcI |
| RA | CP006881 | 3,725,010 | C→T | E53E (GAG→GAA) | U712_19205 ← | Uncharacterized protein ywcI |
| RA | CP006881 | 3,725,025 | A→G | L48L (CTT→CTC) | U712_19205 ← | Uncharacterized protein ywcI |
| RA | CP006881 | 3,725,031 | C→T | A46A (GCG→GCA) | U712_19205 ← | Uncharacterized protein ywcI |
| RA | CP006881 | 3,725,043 | C→A | A42A (GCG→GCT) | U712_19205 ← | Uncharacterized protein ywcI |
| RA | CP006881 | 3,725,049 | T→C | K40K (AAA→AAG) | U712_19205 ← | Uncharacterized protein ywcI |
| RA | CP006881 | 3,725,082 | A→C | A29A (GCT→GCG) | U712_19205 ← | Uncharacterized protein ywcI |
| RA | CP006881 | 3,725,209 | +T | intergenic (‑41/‑488) | U712_19205 ← / → U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| RA | CP006881 | 3,725,237 | A→G | intergenic (‑69/‑460) | U712_19205 ← / → U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| RA | CP006881 | 3,725,239 | 2 bp→AA | intergenic (‑71/‑457) | U712_19205 ← / → U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| RA | CP006881 | 3,772,635 | A→G | Y334C (TAT→TGT) | U712_19455 → | Protein dltB |
| RA | pSIJ663_pHT315_araE_xy | 2,214 | C→T | intergenic (–/‑764) | – / → eryR | –/– |
| JC | pSIJ663_pHT315_araE_xy | 2,655 | Δ3 bp | intergenic (–/‑321) | – / → eryR | –/– |
| JC | pSIJ663_pHT315_araE_xy | 3,843 | Δ5 bp | intergenic (+128/‑24) | eryR → / → ampR | –/– |
| RA | pSIJ663_pHT315_araE_xy | 5,049 | C→T | intergenic (+318/–) | ampR → / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP006881 | 245170 | 246106 | 937 | 30 [22] | [24] 27 | [U712_01140]–[U712_01145] | [U712_01140],[U712_01145] |
| * | * | ÷ | CP006881 | 1067437 | 1068637 | 1201 | 26 [25] | [25] 26 | U712_05250 | U712_05250 |
| * | * | ÷ | CP006881 | 1149042 | 1150722 | 1681 | 26 [23] | [25] 28 | U712_05685 | U712_05685 |
| * | * | ÷ | CP006881 | 1503053 | 1504649 | 1597 | 30 [24] | [22] 27 | U712_07740 | U712_07740 |
| * | * | ÷ | CP006881 | 1562246 | 1566626 | 4381 | 26 [25] | [25] 30 | U712_08060 | U712_08060 |
| * | * | ÷ | CP006881 | 3303154–3303321 | 3304612 | 1292–1459 | 40 [20] | [0] 65 | [U712_16990]–[U712_16995] | [U712_16990],[U712_16995] |
| * | * | ÷ | CP006881 | 3725697 | 3728135 | 2439 | 32 [25] | [24] 28 | [U712_19210] | [U712_19210] |
| * | * | ÷ | CP006881 | 3757680 | 3759669 | 1990 | 30 [23] | [25] 26 | U712_19375 | U712_19375 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP006881 | 390833 = | 100 (1.000) | 148 (1.470) | 63/250 | 0.1 | 62.5% | coding (3098/10752 nt) | U712_01810 | Surfactin synthase subunit 2 |
| ? | CP006881 | = 1080730 | 78 (0.780) | intergenic (+9/+38) | U712_05320/U712_05325 | Competence transcription factor/putative oxidoreductase yhxD | |||||
| * | ? | CP006881 | = 449675 | 102 (1.020) | 83 (0.860) | 39/240 | 0.6 | 51.9% | intergenic (+132/‑1935) | U712_02060/U712_02070 | Uncharacterized protein ycnL/Mannitol‑1‑phosphate 5‑dehydrogenase |
| ? | CP006881 | 1080118 = | 56 (0.580) | intergenic (‑268/‑25) | U712_05315/U712_05320 | Uncharacterized protein yhzC/Competence transcription factor | |||||
| * | ? | CP006881 | 3304613 = | 0 (0.000) | 36 (0.030) +50 bp |
22/150 | 0.8 | 95.2% | intergenic (+1/+48) | U712_16995/U712_17000 | Arabinose metabolism transcriptional repressor/Uncharacterized protein yvbT |
| ? | pSIJ663_pHT315_araE_xy | 9781 = | 6 (0.000) | intergenic (+5050/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5551 | 45 (0.010) | 4352 (1.110) | 190/240 | 0.0 | 99.0% | intergenic (+820/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9889 = | NA (NA) | intergenic (+5158/–) | ampR/– | –/– | |||||