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 | 125,619 | C→T | R21C (CGT→TGT) | U712_00560 → | DNA‑directed RNA polymerase subunit beta' |
| RA | CP006881 | 578,474 | G→A | R61R (CGC→CGT) | U712_02845 ← | UPF0721 transmembrane protein ydhB |
| RA | CP006881 | 907,728 | G→T | G70C (GGT→TGT) | U712_04440 → | Peroxide operon regulator |
| RA | CP006881 | 1,666,671 | T→A | L321* (TTA→TAA) | U712_08575 → | Flagellar motor switch phosphatase FliY |
| 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 | 3,578,472 | (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 | 3,892,629 | C→T | E12K (GAA→AAA) | U712_20070 ← | Inosose isomerase |
| RA | pSIJ663_pHT315_araE_xy | 2,039 | C→T | intergenic (–/‑939) | – / → 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 → / – | –/– |
| RA | pSIJ663_pHT315_araE_xy | 5,205 | G→A | intergenic (+474/–) | ampR → / – | –/– |
| RA | pSIJ663_pHT315_araE_xy | 5,478 | G→A | intergenic (+747/–) | ampR → / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP006881 | 245170 | 246099 | 930 | 47 [26] | [28] 29 | [U712_01140]–[U712_01145] | [U712_01140],[U712_01145] |
| * | * | ÷ | CP006881 | 1067434 | 1068642 | 1209 | 30 [27] | [24] 29 | U712_05250 | U712_05250 |
| * | * | ÷ | CP006881 | 1149053 | 1150720 | 1668 | 31 [26] | [28] 30 | U712_05685 | U712_05685 |
| * | * | ÷ | CP006881 | 1503058 | 1504650 | 1593 | 30 [27] | [26] 29 | U712_07740 | U712_07740 |
| * | * | ÷ | CP006881 | 1562243 | 1566625 | 4383 | 29 [28] | [27] 32 | U712_08060 | U712_08060 |
| * | * | ÷ | CP006881 | 2261293 | 2262067 | 775 | 29 [21] | [23] 29 | U712_11400 | U712_11400 |
| * | * | ÷ | CP006881 | 3303135–3303322 | 3304615 | 1294–1481 | 31 [28] | [1] 47 | [U712_16990]–U712_16995 | [U712_16990],U712_16995 |
| * | * | ÷ | CP006881 | 3725697 | 3728128 | 2432 | 34 [27] | [26] 30 | [U712_19210] | [U712_19210] |
| * | * | ÷ | CP006881 | 3757680 | 3759663 | 1984 | 30 [26] | [28] 30 | U712_19375 | U712_19375 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP006881 | 390833 = | 73 (0.660) | 116 (1.050) | 57/252 | 0.2 | 56.2% | coding (3098/10752 nt) | U712_01810 | Surfactin synthase subunit 2 |
| ? | CP006881 | = 1080730 | 108 (0.980) | intergenic (+9/+38) | U712_05320/U712_05325 | Competence transcription factor/putative oxidoreductase yhxD | |||||
| * | ? | CP006881 | = 449675 | 102 (0.930) | 111 (1.050) | 46/242 | 0.5 | 57.7% | intergenic (+132/‑1935) | U712_02060/U712_02070 | Uncharacterized protein ycnL/Mannitol‑1‑phosphate 5‑dehydrogenase |
| ? | CP006881 | 1080118 = | 65 (0.620) | intergenic (‑268/‑25) | U712_05315/U712_05320 | Uncharacterized protein yhzC/Competence transcription factor | |||||
| * | ? | CP006881 | 2228866 = | 126 (1.150) | 46 (0.430) | 25/246 | 1.9 | 42.6% | intergenic (‑118/‑88) | U712_11195/U712_11200 | Uncharacterized protein ypzE/D‑3‑phosphoglycerate dehydrogenase |
| ? | CP006881 | 3304616 = | 1 (0.010) | intergenic (+4/+45) | U712_16995/U712_17000 | Arabinose metabolism transcriptional repressor/Uncharacterized protein yvbT | |||||
| * | ? | CP006881 | = 2228918 | 140 (1.270) | 80 (0.050) | 26/252 | 1.9 | 36.4% | intergenic (‑170/‑36) | U712_11195/U712_11200 | Uncharacterized protein ypzE/D‑3‑phosphoglycerate dehydrogenase |
| ? | pSIJ663_pHT315_araE_xy | 9781 = | NA (NA) | intergenic (+5050/–) | ampR/– | –/– | |||||