mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 76,539 | T→G | 6.4% | E254A (GAA→GCA) | sgrR ← | transcriptional DNA‑binding transcriptional activator of sgrS sRNA |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 708,109 | A→G | 5.3% | intergenic (+352/‑225) | glnS → / → chiP | glutamyl‑tRNA synthetase/chitoporin, uptake of chitosugars |
| RA | 930,957 | A→C | 5.7% | N2K (AAT→AAG) | cydD ← | glutathione/cysteine ABC transporter export permease/ATPase |
| RA | 1,269,450 | C→T | 5.3% | intergenic (+61/+253) | rdlA → / ← ldrB | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA/toxic polypeptide, small |
| RA | 1,269,612 | T→A | 5.2% | intergenic (+223/+91) | rdlA → / ← ldrB | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA/toxic polypeptide, small |
| JC JC | 1,292,997 | IS2 (–) +5 bp | 70.2% | intergenic (‑75/‑526) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| JC JC | 1,293,004 | IS1 (–) +9 bp | 72.0% | intergenic (‑82/‑515) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| JC JC | 1,293,074 | IS1 (+) +9 bp | 16.5% | intergenic (‑152/‑445) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| JC JC | 1,293,196 | IS5 (+) +4 bp | 13.1% | intergenic (‑274/‑328) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,343,516 | A→C | 5.5% | intergenic (‑188/+81) | osmB ← / ← yciT | osmotically and stress inducible lipoprotein/global regulator of transcription; DeoR family |
| RA | 1,466,210 | G→A | 6.2% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,604 | G→A | 8.5% | pseudogene (1213/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,729 | G→A | 5.3% | pseudogene (1338/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,703,098 | A→C | 31.1% | H289P (CAC→CCC) | add → | adenosine deaminase |
| RA | 1,708,930 | C→A | 12.6% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| JC JC | 2,052,434 | IS1 (–) +9 bp | 13.6% | pseudogene (887‑895/1053 nt) | yeeL ← | pseudogene, glycosyltransferase homology |
| RA | 2,075,512 | T→G | 5.3% | L245R (CTG→CGG) | yeeR → | CP4‑44 prophage; putative membrane protein |
| 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 |
| JC JC | 2,224,288 | IS5 (+) +4 bp | 8.9% | coding (580‑583/933 nt) | pbpG ← | D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,323,353 | T→G | 8.4% | intergenic (+102/‑94) | atoC → / → atoD | fused response regulator of ato operon, in two‑component system with AtoS: response regulator/sigma54 interaction protein/acetyl‑CoA:acetoacetyl‑CoA transferase, alpha subunit |
| RA | 2,649,866 | G→C | 5.8% | L808V (CTG→GTG) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,809,761 | G→T | 6.8% | E49* (GAA→TAA) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 3,006,859 | A→C | 100% | S200R (AGC→CGC) | ygeW → | putative carbamoyltransferase |
| RA | 3,233,264 | A→G | 7.7% | I534V (ATC→GTC) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| 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 |
| RA | 3,577,196 | T→G | 5.8% | M133L (ATG→CTG) | gntK ← | gluconate kinase 2 |
| RA | 3,697,854 | A→C | 5.5% | Q466P (CAA→CCA) | bcsE → | cellulose production protein |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC | 4,001,527 | +GACGAC | 34.5% | coding (102/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| JC | 4,001,538 | Δ99 bp | 15.3% | coding (113‑211/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,002,011 | C→T | 27.7% | Q196* (CAG→TAG) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,002,319:1 | +A | 8.6% | coding (894/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,183,258 | G→A | 100% | E672K (GAA→AAA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,190 | A→G | 21.6% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 23.3% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 17.1% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 5.4% | intergenic (+492/+150) | 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 new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 381689 | NA (NA) | 8 (0.060) | 6/530 | NT | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 75 (0.540) | 77 (0.590) | 57/516 | NT | 56.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 50 (0.380) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 72 (0.520) | 90 (0.690) | 58/516 | NT | 60.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 50 (0.380) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 94 (0.690) | 60/540 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1630598 = | 90 (0.650) | 9 (0.060) | 9/548 | NT | 9.1% | coding (316/1461 nt) | ydfI | putative NAD‑dependent D‑mannonate oxidoreductase |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 79 (0.590) | 59/532 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||