mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 288,136:1 | +A | 5.4% | coding (1348/1611 nt) | yagH → | CP4‑6 prophage; putative xylosidase/arabinosidase |
| RA | 288,136:2 | +G | 5.4% | coding (1348/1611 nt) | yagH → | CP4‑6 prophage; putative xylosidase/arabinosidase |
| RA | 288,136:3 | +C | 5.4% | coding (1348/1611 nt) | yagH → | CP4‑6 prophage; putative xylosidase/arabinosidase |
| RA | 433,649 | T→G | 19.2% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 88.9% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 530,732 | A→C | 19.2% | G165G (GGT→GGG) | mnmH ← | tRNA 2‑selenouridine synthase, selenophosphate‑dependent |
| RA | 540,558 | T→G | 29.7% | intergenic (+50/‑7) | allB → / → ybbY | allantoinase/putative uracil/xanthine transporter |
| RA | 649,766 | T→G | 12.4% | N242T (AAC→ACC) | citE ← | citrate lyase, citryl‑ACP lyase (beta) subunit |
| RA | 1,143,829 | A→C | 12.4% | L180R (CTG→CGG) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,196,305 | C→T | 88.9% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| 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 | 1,466,201 | T→C | 5.7% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,856 | A→G | 5.5% | pseudogene (1465/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,676,805 | T→G | 14.3% | T367P (ACC→CCC) | pntA ← | pyridine nucleotide transhydrogenase, alpha subunit |
| 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 | 2,151,689 | G→T | 31.7% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related 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 |
| RA | 2,312,117 | A→C | 17.8% | G211G (GGT→GGG) | ompC ← | outer membrane porin protein C |
| JC JC | 2,536,312 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | 7.0% | coding (479‑484/510 nt) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 2,828,506 | T→G | 18.5% | V257G (GTG→GGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 3,206,438 | G→A | 19.1% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,469 | A→G | 15.5% | S3G (AGC→GGC) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,483 | G→A | 28.1% | K7K (AAG→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,506 | C→A | 14.4% | T15K (ACA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,285,877 | C→G | 15.6% | P134A (CCG→GCG) | agaD → | N‑acetylgalactosamine‑specific enzyme IID component of PTS |
| 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 | 3,862,661 | T→G | 42.2% | pseudogene (943/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 3,895,556 | T→C | 15.1% | M352V (ATG→GTG) | adeP ← | adenine permease, high affinity; adenine:H+ symporter |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,065,596 | C→A | 16.9% | L57L (CTG→CTT) | yihO ← | putative sulphoquinovose importer |
| RA | 4,094,415 | T→G | 6.2% | intergenic (‑143/+308) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,151,329 | T→G | 16.9% | A590A (GCA→GCC) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,151,332 | G→C | 16.5% | G589G (GGC→GGG) | ppc ← | phosphoenolpyruvate carboxylase |
| JC JC | 4,160,853 | IS2 (+) +5 bp | 11.0% | intergenic (‑63/‑267) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,205,621 | G→T | 26.0% | S104* (TCA→TAA) | purD ← | phosphoribosylglycinamide synthetase phosphoribosylamine‑glycine ligase |
| RA | 4,209,827 | T→G | 13.3% | noncoding (54/76 nt) | gltV → | tRNA‑Glu |
| RA | 4,296,060 | C→T | 21.1% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +C | 93.9% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:2 | +G | 93.9% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,325,948 | A→G | 6.3% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,606,902 | A→G | 14.9% | S267P (TCC→CCC) | rsmC ← | 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 4233726 | 4235454 | 1729 | 36 [35] | [32] 36 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 33 (0.340) | 66 (0.720) | 47/398 | NT | 69.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 28 (0.310) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 34 (0.350) | 77 (0.840) | 46/398 | NT | 72.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 28 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 28 (0.300) | 24/414 | 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 | |||||
| * | ? | NC_000913 | 2449191 = | 58 (0.590) | 3 (0.030) | 3/412 | NT | 5.5% | intergenic (+34/+37) | smrB/yfcO | putative DNA endonuclease/DUF2544 family putative outer membrane protein |
| ? | NC_000913 | 2449213 = | 48 (0.510) | intergenic (+56/+15) | smrB/yfcO | putative DNA endonuclease/DUF2544 family putative outer membrane protein | |||||
| * | ? | NC_000913 | 3984220 = | NA (NA) | 3 (0.030) | 3/416 | NT | NA | noncoding (1/104 nt) | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 3984250 = | NA (NA) | noncoding (31/104 nt) | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP287 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 4542682 = | 28 (0.280) | 3 (0.030) | 3/412 | NT | 5.4% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 79 (0.840) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||