mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| RA | 151,722 | Δ1 bp | 6.7% | coding (510/606 nt) | yadL ← | putative fimbrial‑like adhesin protein |
| RA | 153,785 | T→A | 7.7% | S548C (AGT→TGT) | htrE ← | putative outer membrane usher protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 264,098 | G→T | 100% | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 275,065 | G→A | 100% | T18I (ACC→ATC) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 328,295 | C→T | 5.3% | A147T (GCA→ACA) | betB ← | betaine aldehyde dehydrogenase, NAD‑dependent |
| RA | 386,311 | G→A | 5.5% | P35P (CCG→CCA) | tauB → | taurine ABC transporter ATPase |
| RA | 389,919:1 | +T | 100% | intergenic (‑192/‑332) | hemB ← / → yaiT | 5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| RA | 482,230 | G→A | 100% | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| RA | 495,716 | A→G | 5.5% | K199K (AAA→AAG) | htpG → | protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent; heat‑shock protein; ATPase |
| RA | 654,773 | T→C | 6.6% | Q399R (CAG→CGG) | dcuC ← | anaerobic C4‑dicarboxylate transport |
| RA | 1,075,277 | A→G | 6.6% | D1202D (GAT→GAC) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,158,559 | C→T | 100% | Q231* (CAG→TAG) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,182,882 | C→T | 7.2% | A247T (GCC→ACC) | potC ← | spermidine/putrescine ABC transporter permease |
| RA | 1,196,220 | C→T | 11.6% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | 11.4% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,197,502 | C→T | 100% | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,207,234 | G→T | 7.8% | A108S (GCC→TCC) | ymfQ → | prohage e14 tail protein homolog |
| RA | 1,394,798 | A→G | 8.5% | E524E (GAA→GAG) | mppA → | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| RA | 1,544,021:1 | +A | 76.5% | coding (40/1389 nt) | narU ← | nitrate/nitrite transporter |
| RA | 1,544,022 | C→A | 100% | L13F (TTG→TTT) | narU ← | nitrate/nitrite transporter |
| RA | 1,600,307 | G→T | 9.2% | A312E (GCG→GAG) | lsrR ← | lsr operon transcriptional repressor |
| RA | 1,632,949 | C→T | 11.0% | intergenic (‑664/‑123) | ydfJ ← / → ydfK | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage |
| RA | 1,726,006 | C→A | 33.3% | intergenic (‑86/‑17) | ydhL ← / → nemR | DUF1289 family protein/transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,165 | A→G | 33.0% | Y48C (TAC→TGC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| JC | 1,726,433 | Δ11 bp | 19.5% | coding (411‑421/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,743,514 | C→T | 27.0% | L20F (CTC→TTC) | mdtK → | multidrug efflux system transporter |
| RA | 1,748,487 | A→T | 37.3% | I453F (ATC→TTC) | ydhS → | putative oxidoreductase |
| RA | 1,755,785 | G→T | 34.1% | V30F (GTT→TTT) | pykF → | pyruvate kinase I |
| RA | 1,755,792 | G→T | 35.0% | R32L (CGT→CTT) | pykF → | pyruvate kinase I |
| RA | 1,756,430 | G→T | 32.4% | G245C (GGC→TGC) | pykF → | pyruvate kinase I |
| RA | 1,774,576 | G→A | 100% | G263E (GGG→GAG) | ydiB → | quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding |
| RA | 1,864,768 | T→C | 14.7% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,032,046 | T→C | 9.8% | D91G (GAT→GGT) | dcm ← | DNA cytosine methyltransferase |
| RA | 2,106,741 | A→T | 100% | S162S (TCT→TCA) | wbbH ← | O‑antigen polymerase |
| RA | 2,131,993 | C→T | 5.6% | A26A (GCG→GCA) | wcaC ← | 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 | 2,304,636 | C→G | 11.8% | intergenic (+243/+472) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,556,734 | G→A | 8.3% | G188G (GGC→GGT) | eutC ← | ethanolamine ammonia‑lyase, small subunit (light chain) |
| RA | 2,679,525 | G→T | 100% | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,755,548 | C→T | 6.3% | intergenic (+170/‑611) | smpB → / → intA | tmRNA‑binding trans‑translation protein/CP4‑57 prophage; integrase |
| RA | 2,795,396 | C→A | 100% | Q382K (CAG→AAG) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,817,170 | C→A | 100% | E112* (GAA→TAA) | yqaB ← | fructose‑1‑P and 6‑phosphogluconate phosphatase |
| RA | 2,884,257 | C→A | 10.1% | intergenic (‑119/+296) | casA ← / ← ygcB | CRISP RNA (crRNA) containing Cascade antiviral complex protein/Cascade complex anti‑viral R‑loop helicase‑annealase Cas3 |
| RA | 2,976,638 | T→G | 100% | S14A (TCA→GCA) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 3,270,030 | T→C | 10.4% | intergenic (+428/+186) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| 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 | 3,905,355 | G→A | 7.4% | D81D (GAC→GAT) | bglF ← | fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 3,909,054 | A→G | 5.6% | L129P (CTC→CCC) | pstA ← | phosphate ABC transporter permease |
| RA | 3,946,140 | G→T | 11.1% | noncoding (2437/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,144 | T→C | 13.3% | noncoding (2441/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,161 | G→T | 9.8% | noncoding (2458/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,164 | A→C | 9.3% | noncoding (2461/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,165 | C→T | 9.6% | noncoding (2462/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,180 | T→C | 10.2% | noncoding (2477/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,191 | G→A | 8.3% | noncoding (2488/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,192 | T→G | 7.6% | noncoding (2489/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,219 | A→G | 8.6% | noncoding (2516/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,233 | A→T | 9.2% | noncoding (2530/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,237 | A→C | 7.5% | noncoding (2534/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,241 | C→T | 7.9% | noncoding (2538/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,250 | A→T | 8.4% | noncoding (2547/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,251 | T→G | 8.6% | noncoding (2548/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,263 | A→C | 7.9% | noncoding (2560/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,264 | T→A | 11.2% | noncoding (2561/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,271 | T→C | 9.2% | noncoding (2568/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,289 | T→C | 7.1% | noncoding (2586/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,946,309 | C→T | 9.4% | noncoding (2606/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 4,001,994 | T→C | 6.1% | L190P (CTG→CCG) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,094,415 | T→G | 6.9% | intergenic (‑143/+308) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,111,662 | G→A | 14.6% | L179L (CTG→TTG) | yiiQ ← | DUF1454 family putative periplasmic protein |
| RA | 4,183,136 | G→T | 100% | R637L (CGT→CTT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,193,537 | G→A | 5.1% | R8C (CGT→TGT) | thiF ← | adenylyltransferase, modifies ThiS C‑terminus |
| RA | 4,296,042 | C→T | 25.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,362:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,326,070 | T→G | 6.8% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,604,698 | C→A | 100% | A186E (GCA→GAA) | bglJ → | bgl operon transcriptional activator |
| RA | 4,614,360 | A→G | 7.3% | intergenic (+118/+302) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_hsa_tpiA | 3423766–3424525 | 3424525 | 1–760 | 19 [16] | [17] 18 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | 1207790 = | 15 (0.270) | 18 (0.360) | 13/246 | NT | 61.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | 1209619 = | 9 (0.180) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1207805 | 15 (0.270) | 19 (0.380) | 19/246 | NT | 63.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | = 1209602 | 9 (0.180) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1299498 | 0 (0.000) | 51 (0.930) | 42/270 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_hsa_tpiA | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 3287115 | 54 (0.950) | 3 (0.060) | 3/254 | NT | 5.5% | intergenic (+90/‑311) | agaI/yraH | galactosamine‑6‑phosphate isomerase/putative fimbrial‑like adhesin protein |
| ? | NC_000913_3_hsa_tpiA | = 3287131 | 53 (1.030) | intergenic (+106/‑295) | agaI/yraH | galactosamine‑6‑phosphate isomerase/putative fimbrial‑like adhesin protein | |||||