mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.24 revision cd15a9d216e1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 15,395 | G→A | 6.0% | intergenic (+99/‑48) | dnaJ → / → insL‑1 | chaperone Hsp40, co‑chaperone with DnaK/IS186 hypothetical protein |
| JC JC | 16,972 | IS150 (–) +3 bp | 100% | intergenic (‑14/‑514) | mokC ← / → nhaA | regulatory protein for HokC, overlaps CDS of hokC/pH‑dependent sodium/proton antiporter |
| RA | 161,041 | T→G | 100% | N302H (AAC→CAC) | pcnB ← | poly(A) polymerase I |
| RA | 380,188 | A→C | 100% | F239L (TTT→TTG) | araJ ← | predicted transporter |
| RA | 430,835 | C→T | 100% | intergenic (‑48/‑108) | insL‑2 ← / → lon | putative transposase insL for insertion sequence IS186/DNA‑binding ATP‑dependent protease La |
| RA | 475,288 | +G | 100% | coding (18/1677 nt) | ybaL ← | predicted transporter with NAD(P)‑binding Rossmann‑fold domain |
| MC JC | 547,700 | Δ8,224 bp | 100% | IS1‑mediated | [nmpC]–[ECB_00513] | [nmpC], ybcR, ybcS, ybcT, ybcU, ECB_00510, nohB, ECB_00512, [ECB_00513] |
| RA | 649,391 | T→A | 100% | I471F (ATC→TTC) | mrdA ← | transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2) |
| RA | 668,787 | A→C | 100% | Y65D (TAC→GAC) | gltI ← | glutamate and aspartate transporter subunit |
| RA | 683,496 | A→C | 100% | V65G (GTT→GGT) | nagC ← | DNA‑binding transcriptional dual regulator, repressor of N‑acetylglucosamine |
| RA | 910,316 | T→C | 100% | intergenic (+176/‑175) | ybjN → / → potF | predicted oxidoreductase/putrescine transporter subunit: periplasmic‑binding component of ABC superfamily |
| RA | 1,004,251 | T→C | 100% | intergenic (‑177/+425) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl‑tRNA synthetase |
| RA | 1,248,380 | A→C | 100% | D295E (GAT→GAG) | dhaM ← | fused predicted dihydroxyacetone‑specific PTS enzymes: HPr component/EI component |
| RA | 1,286,699 | C→A | 100% | intergenic (+23/‑160) | narI → / → ECB_01206 | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein |
| RA | 1,329,516 | C→T | 100% | H33Y (CAC→TAC) | topA → | DNA topoisomerase I |
| JC JC | 1,733,647 | IS150 (–) +3 bp | 100% | coding (683‑685/1413 nt) | pykF → | pyruvate kinase |
| JC JC | 1,821,525 | IS150 (–) +3 bp | 100% | coding (573‑575/1041 nt) | ynjI ← | predicted inner membrane protein |
| RA | 1,976,879 | T→G | 100% | intergenic (‑57/‑76) | yedW ← / → yedX | predicted DNA‑binding response regulator in two‑component system with YedV/hypothetical protein |
| RA | 2,082,685 | G→A | 100% | A494V (GCT→GTT) | yegI ← | hypothetical protein |
| RA | 2,732,014 | C→A | 34.6% | R91L (CGC→CTC) | hypF ← | carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases |
| JC JC | 3,015,771 | IS150 (–) +4 bp | 98.3% | coding (1192‑1195/1677 nt) | ECB_02816 → | KpsD protein |
| RA | 3,045,069 | G→T | 100% | T312N (ACC→AAC) | yghJ ← | predicted inner membrane lipoprotein |
| RA | 3,155,168 | G→A | 100% | G296S (GGC→AGC) | ebgR → | DNA‑binding transcriptional repressor |
| RA | 3,248,957 | A→T | 100% | D764E (GAT→GAA) | infB ← | translation initiation factor IF‑2 |
| RA | 3,288,092 | G→A | 100% | R57C (CGT→TGT) | arcB ← | hybrid sensory histidine kinase in two‑component regulatory system with ArcA |
| MC JC | 3,289,962 | Δ16 bp | 100% | coding (96‑111/4554 nt) | gltB → | glutamate synthase, large subunit |
| RA | 3,339,158 | A→C | 100% | intergenic (+22/‑4) | yhdG → / → fis | tRNA‑dihydrouridine synthase B/DNA‑binding protein Fis |
| RA | 3,369,432 | T→C | 100% | D50G (GAC→GGC) | rpsD ← | 30S ribosomal protein S4 |
| RA | 3,370,027 | T→A | 100% | K117M (AAG→ATG) | rpsM ← | 30S ribosomal protein S13 |
| RA | 3,483,047 | C→A | 100% | R455S (CGC→AGC) | malT → | transcriptional regulator MalT |
| RA | 3,490,112 | C→T | 100% | A105T (GCG→ACG) | glpE ← | thiosulfate sulfurtransferase |
| RA | 3,762,741 | A→T | 100% | K662I (AAA→ATA) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,875,625 | +T | 100% | intergenic (‑59/+294) | glmU ← / ← atpC | bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon |
| MC JC | 3,894,997 | Δ6,934 bp | 100% | IS150‑mediated | rbsD–[yieO] | rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO] |
| RA | 4,100,655 | C→T | 100% | M192I (ATG→ATA) | hslU ← | ATP‑dependent protease ATP‑binding subunit |
| RA | 4,126,699 | Δ1 bp | 100% | coding (335/879 nt) | pflC → | pyruvate formate lyase II activase |
| RA | 4,201,911 | C→T | 100% | A217T (GCG→ACG) | iclR ← | DNA‑binding transcriptional repressor |
| JC JC | 4,524,522 | IS186 (+) +6 bp | 98.5% | coding (494‑499/549 nt) | fimA → | major type 1 subunit fimbrin (pilin) |
| RA | 4,616,396 | G→A | 100% | G290S (GGC→AGC) | nadR → | nicotinamide‑nucleotide adenylyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | REL606 | 558866 | 558913 | 48 | 8 [7] | [6] 8 | ECB_00517/appY | conserved hypothetical protein/DNA‑binding transcriptional activator |
| * | * | ÷ | REL606 | 2031681–2031702 | 2035058–2034324 | 2623–3378 | 8 [7] | [0] 14 | [manB]–insA‑14 | [manB], manC, insB‑14, insA‑14 |
| * | * | ÷ | REL606 | 2035094 | 2054966–2054946 | 19853–19873 | 64 [0] | [7] 10 | [wbbD]–[cpsG] | 19 genes [wbbD], wbbC, wzy, wbbB, wbbA, vioB, vioA, wzx, rmlC, rfbA, rfbD, rfbB, galF, wcaM, wcaL, wcaK, wzxC, wcaJ, [cpsG] |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | REL606 | = 16728 | NA (NA) | 26 (0.680) | 19/60 | NT | 78.8% | noncoding (1343/1343 nt) | IS186 | repeat region |
| ? | REL606 | 2713428 = | 7 (0.160) | noncoding (77/93 nt) | serV | tRNA‑Ser | |||||
| * | ? | REL606 | = 16728 | NA (NA) | 4 (0.100) | 4/60 | NT | 14.3% | noncoding (1343/1343 nt) | IS186 | repeat region |
| ? | REL606 | 2448493 = | 24 (0.530) | intergenic (+24/+26) | nupC/yfeA | nucleoside (except guanosine) transporter/predicted diguanylate cyclase | |||||
| * | ? | REL606 | = 23727 | 0 (0.000) | 36 (0.880) | 24/64 | NT | 100% | noncoding (437/768 nt) | IS1 | repeat region |
| ? | REL606 | = 666130 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | REL606 | 241691 = | 0 (0.000) | 46 (1.090) | 29/66 | NT | 100% | noncoding (435/768 nt) | IS1 | repeat region |
| ? | REL606 | 3893554 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | REL606 | 588495 = | NA (NA) | 40 (0.940) | 30/66 | NT | 100% | noncoding (1/1977 nt) | IS150 | repeat region |
| ? | REL606 | 1270660 = | 0 (0.000) | intergenic (‑167/+238) | ldrC/chaA | toxic polypeptide, small/calcium/sodium:proton antiporter | |||||
| * | ? | REL606 | = 590471 | NA (NA) | 26 (0.610) | 20/66 | NT | 81.2% | noncoding (1977/1977 nt) | IS150 | repeat region |
| ? | REL606 | = 3630716 | 6 (0.130) | intergenic (‑171/‑305) | ldrD/yhjV | toxic polypeptide, small/predicted transporter | |||||
| * | ? | REL606 | = 701447 | 39 (1.050) | 8 (0.220) | 4/58 | NT | 19.3% | coding (1109/2199 nt) | speF | ornithine decarboxylase isozyme, inducible |
| ? | REL606 | 3424883 = | 28 (0.620) | intergenic (+101/‑25) | nirD/nirC | nitrite reductase small subunit/nitrite transporter | |||||
| * | ? | REL606 | 1286706 = | 15 (0.400) | 9 (0.240) | 4/58 | NT | 32.7% | intergenic (+30/‑153) | narI/ECB_01206 | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein |
| ? | REL606 | = 2780684 | 22 (0.490) | intergenic (‑286/‑30) | cysJ/ygcM | sulfite reductase, alpha subunit, flavoprotein/6‑pyruvoyl tetrahydrobiopterin synthase (PTPS) | |||||
| * | ? | REL606 | 1290519 = | 16 (0.450) | 5 (0.140) | 3/56 | NT | 29.4% | coding (484/1014 nt) | hnr | response regulator of RpoS |
| ? | REL606 | = 1977651 | 8 (0.180) | coding (175/1005 nt) | yedY | hypothetical protein | |||||
| * | ? | REL606 | = 1977658 | 9 (0.250) | 6 (0.170) | 4/56 | NT | 24.0% | coding (182/1005 nt) | yedY | hypothetical protein |
| ? | REL606 | 3323381 = | 29 (0.650) | coding (769/3801 nt) | yhdP | conserved membrane protein, predicted transporter | |||||
| * | ? | REL606 | = 3571666 | 23 (0.600) | 4 (0.100) | 4/60 | NT | 16.0% | coding (115/1470 nt) | yhiP | predicted transporter |
| ? | REL606 | 3944634 = | 19 (0.420) | intergenic (+23/‑124) | proM/aslB | tRNA‑Pro/predicted regulator of arylsulfatase activity | |||||