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 |
| JC JC | 308,899 | IS2 (+) +5 bp | coding (430‑434/2526 nt) | ecpC ← | putative fimbrial usher protein EcpC |
| 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 | 811,531 | G→A | G384D (GGT→GAT) V4I (GTT→ATT) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase malonyl‑acyl carrier protein methyltransferase |
| RA | 925,196 | G→T | D645Y (GAC→TAC) | clpA → | ATP‑dependent Clp protease ATP‑binding subunit ClpA |
| RA | 1,097,494 | T→A | intergenic (+665/+71) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| 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 | 1,301,992 | 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 |
| JC | 1,399,268 | +CTC | coding (259/753 nt) | fnr ← | DNA‑binding transcriptional dual regulator FNR |
| 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 |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| 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 |
| JC JC | 2,176,322 | IS1 (–) +9 bp | intergenic (‑1/+20) | gatZ ← / ← gatY | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone/tagatose‑1,6‑bisphosphate aldolase 2 |
| RA | 2,406,504 | C→T | M46I (ATG→ATA) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| 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 | 3,938,653 | IS2 (–) +5 bp | coding (427‑431/993 nt) | rbsR → | DNA‑binding transcriptional dual regulator RbsR |
| 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 | 4,566,642 | G→A | S202L (TCG→TTG) | yjiN ← | DUF445 domain‑containing protein YjiN |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423755–3424235 | 3424427–3424237 | 3–673 | 42 [41] | [41] 42 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4035363–4035731 | 4036920–4035735 | 5–1558 | 43 [41] | [39] 43 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 146734 = | 101 (0.900) | 45 (0.400) | 36/598 | 2.3 | 30.8% | intergenic (‑40/‑234) | panD/rpnC | aspartate 1‑decarboxylase proenzyme/recombination‑promoting nuclease RpnC |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 1034134 = | 44 (0.390) | 47 (0.420) | 31/594 | 2.9 | 51.6% | coding (881/1794 nt) | hyaB | hydrogenase 1 large subunit |
| ? | NC_000913 | 1469296 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 1034135 | 44 (0.390) | 76 (0.680) | 52/598 | 1.0 | 63.3% | coding (882/1794 nt) | hyaB | hydrogenase 1 large subunit |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 64 (0.570) | 61 (0.570) | 42/566 | 1.5 | 48.3% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 70 (0.660) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 61 (0.540) | 54 (0.510) | 40/566 | 1.7 | 45.8% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 70 (0.660) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 80 (0.710) | 73 (0.660) | 52/590 | 1.0 | 47.4% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 83 (0.750) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 52 (0.460) | 38/598 | 2.1 | 42.3% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 4348852 = | 71 (0.630) | intergenic (‑108/+463) | dcuB/dcuR | anaerobic C4‑dicarboxylate transporter DcuB/DNA‑binding transcriptional activator DcuR | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 64 (0.570) | 49/594 | 1.2 | 53.3% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 2698402 = | 56 (0.500) | coding (149/636 nt) | pgpC | phosphatidylglycerophosphatase C | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 37 (0.330) | 33/598 | 2.7 | 38.5% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 2698403 | 59 (0.530) | coding (148/636 nt) | pgpC | phosphatidylglycerophosphatase C | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 70 (0.620) | 51/598 | 1.1 | 59.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4542164 | 47 (0.420) | coding (128/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 66 (0.590) | 54/598 | 0.9 | 56.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4542161 = | 50 (0.450) | coding (125/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | = 2698403 | 59 (0.530) | 55 (0.490) | 38/598 | 2.1 | 48.2% | coding (148/636 nt) | pgpC | phosphatidylglycerophosphatase C |
| ? | NC_000913 | = 4508679 | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 3533776 = | 35 (0.310) | 94 (0.840) | 67/594 | 0.4 | 72.9% | coding (959/1623 nt) | pck | phosphoenolpyruvate carboxykinase (ATP) |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 3533777 | 36 (0.320) | 59 (0.530) | 43/598 | 1.6 | 62.1% | coding (960/1623 nt) | pck | phosphoenolpyruvate carboxykinase (ATP) |
| ? | NC_000913 | = 4508679 | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 4348853 | 73 (0.650) | 73 (0.650) | 55/596 | 0.8 | 50.0% | intergenic (‑109/+462) | dcuB/dcuR | anaerobic C4‑dicarboxylate transporter DcuB/DNA‑binding transcriptional activator DcuR |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 4507459 = | NA (NA) | 75 (0.670) | 52/594 | 1.0 | 44.4% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 4640419 | 94 (0.840) | coding (18/141 nt) | yjjY | uncharacterized protein YjjY | |||||
| * | ? | NC_000913 | = 4508679 | NA (NA) | 61 (0.540) | 43/596 | 1.6 | 38.4% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 4640418 = | 98 (0.880) | coding (17/141 nt) | yjjY | uncharacterized protein YjjY | |||||
| * | ? | NC_000913 | 4542682 = | 98 (0.870) | 92 (0.840) | 59/580 | 0.6 | 52.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 75 (0.690) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 109 (0.970) | 99 (0.910) | 56/580 | 0.7 | 52.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 75 (0.690) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||