mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.24rc1 revision 83e50355436e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| JC JC | 16,972 | IS150 (–) +3 bp | intergenic (‑14/‑514) | mokC ← / → nhaA | regulatory protein for HokC, overlaps CDS of hokC/pH‑dependent sodium/proton antiporter |
| RA | 161,041 | T→G | N302H (AAC→CAC) | pcnB ← | poly(A) polymerase I |
| RA | 380,188 | A→C | F239L (TTT→TTG) | araJ ← | predicted transporter |
| RA | 430,835 | C→T | intergenic (‑48/‑108) | insL‑2 ← / → lon | putative transposase insL for insertion sequence IS186/DNA‑binding ATP‑dependent protease La |
| RA | 475,288 | +G | coding (18/1677 nt) | ybaL ← | predicted transporter with NAD(P)‑binding Rossmann‑fold domain |
| RA | 649,391 | T→A | I471F (ATC→TTC) | mrdA ← | transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2) |
| RA | 668,787 | A→C | Y65D (TAC→GAC) | gltI ← | glutamate and aspartate transporter subunit |
| RA | 683,496 | A→C | V65G (GTT→GGT) | nagC ← | DNA‑binding transcriptional dual regulator, repressor of N‑acetylglucosamine |
| RA | 910,316 | T→C | intergenic (+176/‑175) | ybjN → / → potF | predicted oxidoreductase/putrescine transporter subunit: periplasmic‑binding component of ABC superfamily |
| RA | 1,004,251 | T→C | intergenic (‑177/+425) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl‑tRNA synthetase |
| RA | 1,248,380 | A→C | D295E (GAT→GAG) | dhaM ← | fused predicted dihydroxyacetone‑specific PTS enzymes: HPr component/EI component |
| RA | 1,286,699 | C→A | intergenic (+23/‑160) | narI → / → ECB_01206 | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein |
| RA | 1,329,516 | C→T | H33Y (CAC→TAC) | topA → | DNA topoisomerase I |
| JC JC | 1,733,647 | IS150 (–) +3 bp | coding (683‑685/1413 nt) | pykF → | pyruvate kinase |
| JC JC | 1,821,525 | IS150 (–) +3 bp | coding (573‑575/1041 nt) | ynjI ← | predicted inner membrane protein |
| RA | 1,976,879 | T→G | intergenic (‑57/‑76) | yedW ← / → yedX | predicted DNA‑binding response regulator in two‑component system with YedV/hypothetical protein |
| RA | 2,082,685 | G→A | A494V (GCT→GTT) | yegI ← | hypothetical protein |
| RA | 2,732,014 | C→A | R91L (CGC→CTC) | hypF ← | carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases |
| JC JC | 3,015,771 | IS150 (–) +4 bp | coding (1192‑1195/1677 nt) | ECB_02816 → | KpsD protein |
| RA | 3,045,069 | G→T | T312N (ACC→AAC) | yghJ ← | predicted inner membrane lipoprotein |
| RA | 3,155,168 | G→A | G296S (GGC→AGC) | ebgR → | DNA‑binding transcriptional repressor |
| RA | 3,200,643 | C→A | intergenic (+11/‑245) | tdcR → / → yhaB | DNA‑binding transcriptional activator/hypothetical protein |
| RA | 3,248,957 | A→T | D764E (GAT→GAA) | infB ← | translation initiation factor IF‑2 |
| RA | 3,288,092 | G→A | R57C (CGT→TGT) | arcB ← | hybrid sensory histidine kinase in two‑component regulatory system with ArcA |
| MC JC | 3,289,962 | Δ16 bp | coding (96‑111/4554 nt) | gltB → | glutamate synthase, large subunit |
| RA | 3,339,158 | A→C | intergenic (+22/‑4) | yhdG → / → fis | tRNA‑dihydrouridine synthase B/DNA‑binding protein Fis |
| RA | 3,369,432 | T→C | D50G (GAC→GGC) | rpsD ← | 30S ribosomal protein S4 |
| RA | 3,370,027 | T→A | K117M (AAG→ATG) | rpsM ← | 30S ribosomal protein S13 |
| RA | 3,483,047 | C→A | R455S (CGC→AGC) | malT → | transcriptional regulator MalT |
| RA | 3,490,112 | C→T | A105T (GCG→ACG) | glpE ← | thiosulfate sulfurtransferase |
| RA | 3,762,741 | A→T | K662I (AAA→ATA) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,875,625 | +T | intergenic (‑59/+294) | glmU ← / ← atpC | bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon |
| RA | 3,893,550 | +G | intergenic (+5/‑51) | kup → / → insJ‑5 | potassium transporter/IS150 hypothetical protein |
| MC JC | 3,894,997 | Δ6,934 bp | IS150‑mediated | rbsD–[yieO] | rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO] |
| RA | 4,100,655 | C→T | M192I (ATG→ATA) | hslU ← | ATP‑dependent protease ATP‑binding subunit |
| RA | 4,126,699 | Δ1 bp | coding (335/879 nt) | pflC → | pyruvate formate lyase II activase |
| RA | 4,201,911 | C→T | A217T (GCG→ACG) | iclR ← | DNA‑binding transcriptional repressor |
| JC JC | 4,524,522 | IS186 (+) +6 bp | coding (494‑499/549 nt) | fimA → | major type 1 subunit fimbrin (pilin) |
| RA | 4,616,396 | G→A | G290S (GGC→AGC) | nadR → | nicotinamide‑nucleotide adenylyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | REL606 | 546958–547700 | 555936–555805 | 8106–8979 | 18 [15] | [15] 16 | [insB‑6]–[ECB_00513] | [insB‑6], insA‑6, nmpC, ybcR, ybcS, ybcT, ybcU, ECB_00510, nohB, ECB_00512, [ECB_00513] |
| * | * | ÷ | REL606 | 2031674–2031721 | 2054972–2054943 | 23223–23299 | 20 [15] | [15] 16 | [manB]–[cpsG] | 23 genes [manB], manC, insB‑14, insA‑14, 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 | = 547699 | NA (NA) | 52 (0.940) | 27/70 | 0.7 | NA | noncoding (1/768 nt) | IS1 | repeat region |
| ? | REL606 | 555924 = | NA (NA) | coding (1209/2346 nt) | ECB_00513 | conserved hypothetical protein | |||||
| * | ? | REL606 | 589886 = | NA (NA) | 37 (0.710) | 21/66 | 1.2 | NA | noncoding (437/768 nt) | IS1 | repeat region |
| ? | REL606 | = 590471 | NA (NA) | noncoding (1977/1977 nt) | IS150 | repeat region | |||||
| * | ? | REL606 | 664688 = | NA (NA) | 35 (0.670) | 24/66 | 0.8 | 100% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | REL606 | 1270660 = | 0 (0.000) | intergenic (‑167/+238) | ldrC/chaA | toxic polypeptide, small/calcium/sodium:proton antiporter | |||||
| * | ? | REL606 | = 3630716 | NA (NA) | 31 (0.560) | 22/70 | 1.2 | NA | intergenic (‑171/‑305) | ldrD/yhjV | toxic polypeptide, small/predicted transporter |
| ? | REL606 | = 3652533 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | REL606 | 3651091 = | NA (NA) | 68 (1.230) | 34/70 | 0.2 | NA | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | REL606 | = 3741531 | NA (NA) | noncoding (435/768 nt) | IS1 | repeat region | |||||