mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 280,920 | T→C | 5.0% | E355G (GAA→GGA) | yagA ← | CP4‑6 prophage, putative DNA‑binding transcriptional regulator |
| RA | 284,128 | A→G | 14.8% | T310A (ACC→GCC) | yagF → | CP4‑6 prophage, dehydratase family protein |
| RA | 327,610:1 | +G | 8.3% | coding (1124/1473 nt) | betB ← | betaine aldehyde dehydrogenase, NAD‑dependent |
| RA | 399,746 | T→C | 6.0% | F52L (TTC→CTC) | yaiZ → | DUF2754 family putative inner membrane protein |
| RA | 508,809 | G→A | 7.9% | intergenic (+250/+66) | ybaQ → / ← copA | putative DNA‑binding transcriptional regulator/copper transporter |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,466,711 | T→C | 17.7% | pseudogene (1320/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,729 | G→A | 15.9% | pseudogene (1338/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,497,102 | A→G | 9.1% | S83G (AGT→GGT) | opgD → | OPG biosynthetic periplasmic protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 3,464,610:1 | +C | 9.5% | coding (691/1164 nt) | gspL → | general secretory pathway component, cryptic |
| RA | 3,528,106 | T→G | 24.0% | L547R (CTG→CGG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,537 | C→A | 24.2% | A34E (GCA→GAA) | yidX → | putative lipoprotein |
| RA | 3,921,196 | T→C | 3.9% | intergenic (‑8/+39) | atpE ← / ← atpB | F0 sector of membrane‑bound ATP synthase, subunit c/F0 sector of membrane‑bound ATP synthase, subunit a |
| RA | 3,992,437 | T→G | 15.4% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 3,992,468 | Δ4 bp | 7.0% | coding (1317‑1320/2547 nt) | cyaA → | adenylate cyclase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,163,493 | C→T | 11.4% | intergenic (‑224/‑145) | trmA ← / → btuB | tRNA m(5)U54 methyltransferase, SAM‑dependent, tmRNA m(5)U341 methyltransferase/vitamin B12/cobalamin outer membrane transporter |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,189 | A→G | 50.6% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 50.2% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533750 | 2536311 | 2562 | 11 [9] | [0] 10 | ptsH–[crr] | ptsH, ptsI, [crr] |
| * | * | ÷ | NC_000913 | 3423905–3424228 | 3424384–3424237 | 10–480 | 11 [9] | [8] 10 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3799021 | 3799497 | 477 | 10 [9] | [9] 12 | [waaU]–[waaZ] | [waaU], [waaZ] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 66 (1.450) | 52/516 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 17 (0.370) | 27 (0.630) | 26/484 | NT | 62.8% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 16 (0.370) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.330) | 37 (0.870) | 26/484 | NT | 71.1% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 16 (0.370) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1287329 | 25 (0.550) | 4 (0.130) | 4/342 | NT | 16.5% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 24 (0.800) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate hydrolase | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.020) | 68 (1.490) | 53/516 | NT | 98.6% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1329019 = | 80 (1.760) | 3 (0.070) | 3/504 | NT | 5.2% | coding (94/759 nt) | yciK | putative EmrKY‑TolC system oxoacyl‑(acyl carrier protein) reductase |
| ? | NC_000913 | 1330035 = | 32 (0.720) | coding (704/1050 nt) | sohB | inner membrane protein, S49 peptidase family protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 26 (0.570) | 22/516 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 47 (1.030) | 34/516 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 35 (0.770) | 32/516 | NT | 68.6% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 3526447 = | 16 (0.350) | intergenic (‑300/‑20) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 22 (0.480) | 22/514 | NT | 61.2% | intergenic (‑31/+2) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| ? | NC_000913 | = 3526451 | 14 (0.310) | intergenic (‑304/‑16) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | 3845530 = | 37 (0.810) | 25 (0.570) | 24/496 | NT | 37.2% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992759 | 49 (1.120) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||