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 |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC JC | 260,173 | Δ13,782 bp | IS5‑mediated | proB–[ykfC] | 19 genes proB, proA, thrW, ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI1, insN, eyeA, [ykfC] |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 635,355 | G→A | R8* (CGA→TGA) N405N (AAC→AAT) |
ybdM ← ybdN ← |
ParB‑like nuclease domain‑containing protein YbdM putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 696,582 | C→T | noncoding (35/75 nt) | glnV ← | tRNA‑Gln |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,296,375 | A→G | F583L (TTC→CTC) | adhE ← | fused acetaldehyde‑CoA dehydrogenase and iron‑dependent alcohol dehydrogenasealdehyde/alcohol dehydrogenase AdhE |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,705,108 | G→A | G54R (GGG→AGG) | cnu → | H‑NS‑ and StpA‑binding protein |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| JC JC | 3,890,570 | IS5 (–) +4 bp | coding (335‑338/1248 nt) | tnaB → | tryptophan:H(+) symporter TnaB |
| RA | 4,132,697 | G→A | E28K (GAG→AAG) | metF → | 5,10‑methylenetetrahydrofolate reductase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,569,394 | T→C | intergenic (‑667/+768) | ytiE ← / ← yjiR | protein YtiE/fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978463 | 1979327 | 865 | 9 [8] | [8] 9 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 4035327–4035733 | 4036872–4035735 | 3–1546 | 10 [8] | [8] 10 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 151626 = | 20 (0.350) | 14 (0.250) | 13/486 | 2.5 | 41.2% | coding (606/606 nt) | yadL | putative fimbrial protein YadL |
| ? | NC_000913 | 273955 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 10 (0.180) | 10/486 | 3.0 | 20.4% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 362204 = | 39 (0.690) | coding (976/1254 nt) | lacY | lactose permease | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 11 (0.190) | 11/486 | 2.8 | 36.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1196827 = | 19 (0.330) | intergenic (+45/+40) | C0293/ymfD | small regulatory RNA C0293/putative SAM‑dependent methyltransferase YmfD | |||||
| * | ? | NC_000913 | = 781688 | 40 (0.700) | 8 (0.180) | 8/378 | 2.8 | 22.8% | intergenic (+36/‑397) | lysQ/nadA | tRNA‑Lys/quinolinate synthase |
| ? | NC_000913 | 781845 = | 23 (0.520) | intergenic (+193/‑240) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 1196830 | 19 (0.330) | 12 (0.210) | 12/486 | 2.6 | 38.7% | intergenic (+48/+37) | C0293/ymfD | small regulatory RNA C0293/putative SAM‑dependent methyltransferase YmfD |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1207805 | 33 (0.580) | 21 (0.400) | 21/454 | 1.4 | 47.3% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 16 (0.300) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299497 | 5 (0.090) | 34 (0.600) | 30/482 | 0.9 | 87.3% | intergenic (+252/‑70) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | = 1300694 | NA (NA) | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 34 (0.630) | 31/462 | 0.8 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300694 = | 0 (0.000) | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1743496 = | 27 (0.470) | 19 (0.330) | 19/486 | 1.7 | 41.3% | coding (40/1374 nt) | mdtK | multidrug efflux pump MdtK |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1743499 | 27 (0.470) | 14 (0.250) | 14/486 | 2.3 | 34.2% | coding (43/1374 nt) | mdtK | multidrug efflux pump MdtK |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 46 (0.810) | 45/486 | 0.3 | 78.0% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2176330 | 13 (0.230) | intergenic (‑9/+20) | gatZ/gatY | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone/tagatose‑1,6‑bisphosphate aldolase 2 | |||||
| * | ? | NC_000913 | = 1979270 | NA (NA) | 45 (0.790) | 41/486 | 0.4 | 75.0% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 2176322 = | 15 (0.260) | intergenic (‑1/+28) | gatZ/gatY | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone/tagatose‑1,6‑bisphosphate aldolase 2 | |||||
| * | ? | NC_000913 | 2098309 = | 26 (0.460) | 12 (0.210) | 10/482 | 2.9 | 31.6% | intergenic (‑8/+138) | wzzB/ugd | O‑antigen co‑polymerase/UDP‑glucose 6‑dehydrogenase |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2098312 | 26 (0.460) | 20 (0.350) | 19/486 | 1.7 | 43.5% | intergenic (‑11/+135) | wzzB/ugd | O‑antigen co‑polymerase/UDP‑glucose 6‑dehydrogenase |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 10 (0.180) | 10/486 | 3.0 | 22.2% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2484281 | 35 (0.620) | coding (527/615 nt) | evgA | DNA‑binding transcriptional activator EvgA | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 13 (0.230) | 13/486 | 2.5 | 43.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2469405 = | 17 (0.300) | coding (275/1332 nt) | yfdI | serotype‑specific glucosyl transferase YfdI | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 11 (0.190) | 10/486 | 3.0 | 25.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3206574 | 33 (0.580) | coding (112/912 nt) | ttdA | L(+)‑tartrate dehydratase subunit alpha | |||||
| * | ? | NC_000913 | = 2558698 | 38 (0.670) | 14 (0.250) | 14/470 | 2.2 | 23.4% | intergenic (‑19/‑160) | eutB/intZ | ethanolamine ammonia‑lyase subunit alpha/putative phage integrase IntZ |
| ? | NC_000913 | 2565489 = | 55 (1.000) | coding (1396/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivase EutA | |||||
| * | ? | NC_000913 | = 3110591 | 12 (0.210) | 16 (0.280) | 16/486 | 2.1 | 57.1% | coding (536/537 nt) | yghD | putative type II secretion system M‑type protein YghD |
| ? | NC_000913 | 3130146 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 13 (0.230) | 12/486 | 2.6 | 27.1% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 3367745 = | 35 (0.620) | intergenic (+103/‑82) | yhcF/yhcG | DUF1120 domain‑containing protein YhcF/DUF1016 domain‑containing protein YhcG | |||||
| * | ? | NC_000913 | = 3187426 | NA (NA) | 20 (0.350) | 19/486 | 1.7 | 35.7% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3367749 | 36 (0.630) | intergenic (+107/‑78) | yhcF/yhcG | DUF1120 domain‑containing protein YhcF/DUF1016 domain‑containing protein YhcG | |||||
| * | ? | NC_000913 | 3652036 = | NA (NA) | 12 (0.210) | 11/486 | 2.8 | 22.2% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3843042 | 42 (0.740) | coding (748/1335 nt) | adeQ | adenine transporter | |||||
| * | ? | NC_000913 | 4117984 = | 34 (0.600) | 11 (0.190) | 11/482 | 2.8 | 24.4% | coding (107/846 nt) | glpF | glycerol facilitator |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 4163082 = | 34 (0.600) | 29 (0.510) | 28/484 | 1.0 | 46.0% | coding (189/1101 nt) | trmA | tRNA m(5)U54 methyltransferase |
| ? | NC_000913 | = 4499511 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 4163086 | 34 (0.600) | 19 (0.340) | 19/484 | 1.7 | 35.9% | coding (185/1101 nt) | trmA | tRNA m(5)U54 methyltransferase |
| ? | NC_000913 | 4498181 = | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||