mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 155,463 | A→T | *247K (TAA→AAA) | yadV ← | putative fimbrial chaperone YadV |
| MC JC | 519,143 | Δ14,682 bp | [ybbO]–[allZ] | [ybbO], [tesA], ybbA, ybbP, rhsD, ybbC, ylbG, selU, allS, allA, [allR], [allZ] | |
| RA | 535,337 | T→C | A474A (GCT→GCC) | gcl → | glyoxylate carboligase |
| RA | 536,173 | T→C | L155P (CTC→CCC) | hyi → | hydroxypyruvate isomerase |
| RA | 536,492 | A→G | intergenic (+6/‑94) | hyi → / → glxR | hydroxypyruvate isomerase/tartronate semialdehyde reductase 2 |
| RA | 536,549 | T→C | intergenic (+63/‑37) | hyi → / → glxR | hydroxypyruvate isomerase/tartronate semialdehyde reductase 2 |
| MC JC | 536,617 | Δ14,712 bp | [glxR]–[ybcF] | [glxR], ybbW, allB, ybbY, glxK, allE, allC, allD, fdrA, ylbE, ylbF, [ybcF] | |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| MC JC | 565,054 | 44181 bp→TGA | [intD]–insL2 | 52 genes [intD], renD, insE3, insF3, renD, emrE, ylcJ, ybcK, ybcL, ybcM, ylcH, ybcN, ninE, ybcO, rusA, ylcG, quuD, nmpC, insH2, nmpC, essD, rrrD, rzpD, rzoD, borD, ybcV, ybcW, ylcI, nohD, tfaD, tfaX, appY, ompT, envY, ybcH, nfrA, nfrB, cusS, cusR, cusC, cusF, cusB, cusA, pheP, ybdG, nfsB, ybdF, ybdJ, ybdK, sokE, hokE, insL2 |
|
| RA | 670,635 | A→T | L324Q (CTG→CAG) | holA ← | DNA polymerase III subunit delta |
| RA | 1,048,596 | G→A | G32G (GGC→GGT) | gfcC ← | capsule biosynthesis GfcC family protein |
| MC JC | 1,048,805 | Δ48,085 bp | [gfcB]–ycdU | 45 genes [gfcB], gfcA, insA4, insB4, cspH, cspG, ymcF, ymcE, gnsA, yccM, torS, torT, torR, torC, torA, torD, cbpM, cbpA, yccE, agp, yccJ, wrbA, ymdF, rutG, rutF, rutE, rutD, rutC, rutB, rutA, rutR, putA, ymdG, putP, efeO, efeB, phoH, pgaD, pgaC, pgaB, pgaA, dgcT, insF4, insE4, ycdU |
|
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,196,861 | A→G | intergenic (+79/+6) | C0293 → / ← ymfD | small regulatory RNA C0293/putative SAM‑dependent methyltransferase YmfD |
| MC JC | 1,196,867 | Δ27,041 bp | [ymfD]–ymgJ | 37 genes [ymfD], ymfE, lit, intE, xisE, ymfH, ymfI, ymfJ, ymfK, ymfT, ymfL, ymfM, ymfN, ymfR, beeE, ymfQ, ycfK, tfaP, tfaE, pinE, mcrA, iraM, ymgK, ymgL, ycgX, bluR, bluF, ycgZ, ymgA, ariR, ymgC, pdeG, ymgF, ymgD, ymgG, ymgI, ymgJ |
|
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,917 | C→T | Q246Y (CAG→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,301,919 | G→T | Q246Y (CAG→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,628,332 | T→C | intergenic (+69/‑20) | ydfG → / → rspR | 3‑hydroxy acid dehydrogenase YdfG/DNA‑binding transcriptional repressor RspR |
| MC JC | 1,628,340 | Δ10,127 bp | rspR–[cspI] | 17 genes rspR, ydfZ, ydfI, ydfJ, ynfT, ydfK, pinQ, tfaQ, stfQ, nohA, ynfO, ydfO, gnsB, ynfN, ynfR, ynfQ, [cspI] |
|
| RA | 1,638,571 | G→A | H33Y (CAT→TAT) | cspI ← | cold shock‑like protein CspI |
| RA | 1,640,045 | +C | coding (13/534 nt) | rrrQ ← | putative lysozyme |
| MC JC | 1,640,057 | Δ7,591 bp | [rrrQ]–[dicC] | 18 genes [rrrQ], [ydfR], essQ, ynfU, cspB, cspF, ynfS, ydfT, ydfU, rem, hokD, relE, relB, ydfV, flxA, ydfW, ydfX, [dicC] |
|
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 2,016,437 | Δ2 bp :: IS186 (–) +8 bp :: Δ1 bp | coding (570‑577/687 nt) | fliH → | flagellar biosynthesis protein FliH |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,529,094 | C→A | A361A (GCG→GCT) | ligA ← | DNA ligase |
| RA | 2,867,454 | 2 bp→AA | coding (97‑98/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| MC JC | 3,110,591 | Δ24,234 bp | [yghD]–yghT | 20 genes [yghD], yghE, yqhJ, yghF, yghG, pppA, yghJ, glcA, glcB, glcG, glcF, glcE, glcD, glcC, yghO, insH9, yghQ, yghR, yghS, yghT |
|
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| JC JC | 3,707,484 | +GA :: IS3 (+) +4 bp | coding (219‑222/1608 nt) | dppA ← | dipeptide ABC transporter periplasmic binding protein |
| JC JC | 3,720,136 | IS3 (–) +3 bp :: +TCA | coding (88‑90/213 nt) | cspA → | cold shock protein CspA |
| JC JC | 3,890,411 | IS1 (–) +9 bp | coding (176‑184/1248 nt) | tnaB → | tryptophan:H(+) symporter TnaB |
| RA | 4,235,651 | T→C | intergenic (+244/‑255) | pgi → / → yjbE | glucose‑6‑phosphate isomerase/uncharacterized protein YjbE |
| MC JC | 4,235,905 | 16376 bp→52 bp | yjbE–malM | yjbE, yjbF, yjbG, yjbH, yjbT, psiE, xylE, malH, malG, malF, malE, malK, lamB, malM | |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| MC JC | 4,299,522 | Δ12,535 bp | mdtP–alsB | mdtP, mdtO, mdtN, ytcA, yjcS, alsK, alsE, alsC, alsA, alsB | |
| RA | 4,312,070 | Δ1 bp | intergenic (‑28/+31) | alsB ← / ← alsR | D‑allose ABC transporter periplasmic binding protein/DNA‑binding transcriptional repressor AlsR |
| RA | 4,312,151 | G→C | Q281E (CAA→GAA) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,312,215 | A→G | T259T (ACT→ACC) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,312,219 | A→G | L258P (CTA→CCA) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,312,289 | A→G | Y235H (TAT→CAT) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,312,498 | C→G | R165P (CGC→CCC) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,313,027 | T→G | intergenic (‑36/‑323) | alsR ← / → rpiB | DNA‑binding transcriptional repressor AlsR/allose‑6‑phosphate isomerase/ribose‑5‑phosphate isomerase B |
| MC JC | 4,313,864 | Δ16,405 bp | yjdP–rdcB | 18 genes yjdP, phnP, phnO, phnN, phnM, phnL, phnK, phnJ, phnI, phnH, phnG, phnF, phnD, phnC, yjdN, yjdM, rdcA, rdcB |
|
| RA | 4,558,907 | T→A | K207M (AAG→ATG) | iadA ← | isoaspartyl dipeptidase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 19 [0] | [0] 18 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 2406788 | 2407179 | 392 | 47 [0] | [0] 34 | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| * | * | ÷ | NC_000913 | 3423885–3424232 | 3424444–3424238 | 7–560 | 4 [3] | [3] 4 | rrlD | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 21 (0.710) | 20/470 | 0.5 | 100% | intergenic (+8/+16) | crl/insB9 | RNA polymerase holoenzyme assembly factor Crl/IS1 family transposase B |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 19 (0.620) | 19/486 | 0.6 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 46 (1.520) | 40/484 | 0.0 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2406787 | 0 (0.000) | intergenic (‑146/‑774) | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 18 (0.590) | 17/486 | 0.7 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | 2407180 = | 0 (0.000) | 34 (1.120) | 32/484 | 0.1 | 100% | intergenic (‑539/‑381) | lrhA/alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| ? | NC_000913 | 3583428 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||