mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
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 | 327,608:1 | +G | 8.3% | coding (1126/1473 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 |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| 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 | 1,466,729 | G→A | 13.4% | 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 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 3,464,611:1 | +C | 9.5% | coding (690/1164 nt) | gspL → | general secretory pathway component, cryptic |
| JC JC | 3,526,449 | IS5 (+) +4 bp | 68.5% | intergenic (‑300/‑17) | nudE ← / → yrfF | adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,528,108 | T→G | 24.0% | L547R (CTG→CGG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,538 | C→A | 24.2% | A34E (GCA→GAA) | yidX → | putative lipoprotein |
| RA | 3,992,438 | T→G | 15.6% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 3,992,469 | Δ4 bp | 7.0% | coding (1317‑1320/2547 nt) | cyaA → | adenylate cyclase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,163,494 | 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 | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,190 | A→G | 34.8% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 33.8% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | 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 | 2533752 | 2536342 | 2591 | 10 [8] | [8] 10 | ptsH–[crr] | ptsH,ptsI,[crr] |
| * | * | ÷ | NC_000913 | 3423907–3424230 | 3424386–3424239 | 10–480 | 11 [9] | [8] 10 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3799022 | 3799498 | 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 | 1207790 = | 17 (0.380) | 27 (0.640) | 26/484 | NT | 62.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 16 (0.380) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.330) | 36 (0.850) | 26/484 | NT | 70.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 16 (0.380) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1287329 | 24 (0.530) | 4 (0.130) | 4/342 | NT | 16.7% | 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 | 1329019 = | 80 (1.770) | 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 | 3845531 = | 37 (0.820) | 23 (0.530) | 22/496 | NT | 35.5% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992760 | 48 (1.100) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||